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arun

2013-Feb-28 19:39 UTC

[R] new question

Hi,
directory<- "/home/arunksa111/data.new"
#first function
filelist<-function(directory,number,list1){
setwd(directory)
filelist1<-dir(directory)
direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep =
"\t",stringsAsFactors=FALSE))
names(list1)<-filelist1
list2<- list(filelist1,list1)
return(list2)
}
foldernames1<-filelist(directory,23,list1)[[1]]
foldernames1
#[1] "a1" "c1" "c2" "c3" "t1"
"t2"
lista<-filelist(directory,23,list1)[[2]] #lista output

FacGroup<- c("c1","c3","t2")

#Second function
f<-function(listRes,Toselect){
res2<-split(listRes,gsub("[0-9]","",names(listRes)))
res3<-lapply(seq_along(res2),function(i) lapply(res2[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
res4<-lapply(res3,function(x) x[names(x)[names(x)%in%Toselect]])
res4New<- lapply(res4,function(x) lapply(names(x), function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x))) ))
library(plyr) 
library(data.table) 
res5<-lapply(res4New,function(x) lapply(x,function(x1){ x1<-
data.table(x1);x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))
res6<- lapply(res5,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
?
res7<-lapply(res6,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
?res8<-res7[lapply(res7,length)!=0] 
?res9<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),res8)
res9[is.na(res9)] <- 0
return(res9)
}

f(lista,FacGroup)
?head(f(lista,FacGroup))
?#??????????????????? Seq??????? Mod z c1 c3 t2
#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 0? 0? 1
#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 0? 0? 1
#3?????? aAAAAAAAAAGAAGGR 1-n_acPro/ 2? 0? 0? 1
#4? aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2? 1? 0? 0
#5??????????? AAAAAAALQAK??????????? 2? 0? 1? 1
#6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2

resCounts<- f(lista,FacGroup)
t.test.p.value <- function(...) { 
??? obj<-try(t.test(...), silent=TRUE) 
??? if (is(obj, "try-error")) return(NA) else return(obj$p.value) 
?}

#3rd function for p-value
fpv<- function(Countdata){
resNew<-do.call(cbind,lapply(split(names(Countdata)[4:ncol(Countdata)],gsub("[0-9]","",names(Countdata)[4:ncol(Countdata)])),
function(i) {x<-if(ncol(Countdata[i])>1) rowSums(Countdata[i]) else
Countdata[i]; colnames(x)<-NULL;x}))
indx<-combn(names(resNew),2) 
resPval<-do.call(cbind,lapply(seq_len(ncol(indx)),function(i)
{x<-as.data.frame(apply(resNew[,indx[,i]],1,t.test.p.value));
colnames(x)<-paste("Pvalue",paste(indx[,i],collapse=""),sep="_");x}))
resF<-cbind(resCounts,resPval)
resF
}

fpv(resCounts)


A.K.





________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, February 28, 2013 11:30 AM
Subject: new question


Sorry about my question, but I need a new small thing...I need to split my
function to read data and to do the treatment of the data.

At first I need to know the "names" of the files and read data, and
after a new function with my analysis.

So, I did this

directory<-"C:/Users/Vera Costa/Desktop/data.new"?
filelist<-function(directory,number){
setwd(directory)
filelist<-dir(directory)
return(filelist)
direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
lista<-lapply(direct, function(x) read.table(x,header=TRUE, sep =
"\t"))
names(lista)<-filelist
return(lista)
}
filelist(directory,23)


###"a1" "a2" "c1" "c2" "c3"
"t1" "t2"



and after 

f<-function(filelist,FacGroup){

res2<-split(lista,names(lista))
?res3<- lapply(res2,function(x)
{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
res3
#Freq FDR<0.01
?res4<-lapply(seq_along(res3),function(i) lapply(res3[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
?names(res4)<- names(res2)
?res4
? res4New<-lapply(res4,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x))) ))
?res5<- lapply(res4New,function(x) if(length(x)>1) tail(x,-1) else NULL)
?library(plyr)
?library(data.table)
?res6<- lapply(res5,function(x) lapply(x,function(x1) {x1<-data.table(x1);
x1[,spec:=past




How can I "ask lista in second function? Could you help me??????????????

arun

2013-Mar-07 15:19 UTC

head link

[R] new question

Hi,


directory<- "/home/arunksa111/dados" #renamed directory to dados
filelist<-function(directory,number,list1){
setwd(directory)
filelist1<-dir(directory)
direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep =
"\t",stringsAsFactors=FALSE))
names(list1)<-filelist1
list2<- list(filelist1,list1)
return(list2)
}
foldernames1<-filelist(directory,23,list1)[[1]]
foldernames1
#[1] "a1" "a2" "c1" "c2" "c3"
"t1" "t2"
lista<-filelist(directory,23,list1)[[2]] #lista output?

#If you look at the 
?lapply(lista,function(x) sapply(x,class)) #some spec were integer, and some
were character
#do this
?listaNew<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))

FacGroup<- c("c1","c3","t2")
#Second function
#f<- function(....)

head(f(listaNew,FacGroup))
#???????????????????? Seq??????? Mod z c1 c3 t2
#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 0? 0? 1
#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 0? 0? 1
#3?????? aAAAAAAAAAGAAGGR 1-n_acPro/ 2? 0? 0? 1
#4? aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2? 1? 0? 0
#5??????????? AAAAAAALQAK??????????? 2? 0? 1? 1
#6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2


A.K.



________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 7, 2013 7:12 AM
Subject: Re: new question


Hi.

Sorry again a question about this, but when I run this code I have this error:

Error in `[.data.table`(x1, , `:=`(spec, paste(spec, collapse =
",")),? :
? Type of RHS ('character') must match LHS ('integer'). To check
and coerce would impact performance too much for the fastest cases. Either
change the type of the target column, or coerce the RHS of := yourself (e.g. by
using 1L instead of 1)

Could you help me to with this? How can I eliminate this?

Thank you




2013/2/28 arun <smartpink111 at yahoo.com>

Hi,>directory<- "/home/arunksa111/data.new"
>#first function
>filelist<-function(directory,number,list1){
>setwd(directory)
>filelist1<-dir(directory)
>
>direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
>list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep =
"\t",stringsAsFactors=FALSE))
>names(list1)<-filelist1
>list2<- list(filelist1,list1)
>return(list2)
>}
>foldernames1<-filelist(directory,23,list1)[[1]]
>foldernames1
>#[1] "a1" "c1" "c2" "c3"
"t1" "t2"
>lista<-filelist(directory,23,list1)[[2]] #lista output
>
>FacGroup<- c("c1","c3","t2")
>
>#Second function
>f<-function(listRes,Toselect){
>res2<-split(listRes,gsub("[0-9]","",names(listRes)))
>res3<-lapply(seq_along(res2),function(i) lapply(res2[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
>res4<-lapply(res3,function(x) x[names(x)[names(x)%in%Toselect]])
>res4New<- lapply(res4,function(x) lapply(names(x), function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x))) ))
>library(plyr)
>library(data.table)
>res5<-lapply(res4New,function(x) lapply(x,function(x1){ x1<-
data.table(x1);x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))
>res6<- lapply(res5,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
>?
>res7<-lapply(res6,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
>?res8<-res7[lapply(res7,length)!=0]
>?res9<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),res8)
>res9[is.na(res9)] <- 0
>return(res9)
>}
>
>f(lista,FacGroup)
>?head(f(lista,FacGroup))
>?#??????????????????? Seq??????? Mod z c1 c3 t2
>#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 0? 0? 1
>#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 0? 0? 1
>#3?????? aAAAAAAAAAGAAGGR 1-n_acPro/ 2? 0? 0? 1
>#4? aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2? 1? 0? 0
>#5??????????? AAAAAAALQAK??????????? 2? 0? 1? 1
>#6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2
>
>resCounts<- f(lista,FacGroup)
>t.test.p.value <- function(...) {
>??? obj<-try(t.test(...), silent=TRUE)
>??? if (is(obj, "try-error")) return(NA) else return(obj$p.value)
>?}
>
>#3rd function for p-value
>fpv<- function(Countdata){
>resNew<-do.call(cbind,lapply(split(names(Countdata)[4:ncol(Countdata)],gsub("[0-9]","",names(Countdata)[4:ncol(Countdata)])),
function(i) {x<-if(ncol(Countdata[i])>1) rowSums(Countdata[i]) else
Countdata[i]; colnames(x)<-NULL;x}))
>indx<-combn(names(resNew),2)
>resPval<-do.call(cbind,lapply(seq_len(ncol(indx)),function(i)
{x<-as.data.frame(apply(resNew[,indx[,i]],1,t.test.p.value));
colnames(x)<-paste("Pvalue",paste(indx[,i],collapse=""),sep="_");x}))
>resF<-cbind(resCounts,resPval)
>resF
>}
>
>fpv(resCounts)
>
>
>A.K.
>
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta.rt at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Thursday, February 28, 2013 11:30 AM
>Subject: new question
>
>
>
>Sorry about my question, but I need a new small thing...I need to split my
function to read data and to do the treatment of the data.
>
>At first I need to know the "names" of the files and read data,
and after a new function with my analysis.
>
>So, I did this
>
>directory<-"C:/Users/Vera Costa/Desktop/data.new"?
>filelist<-function(directory,number){
>setwd(directory)
>filelist<-dir(directory)
>return(filelist)
>direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
>lista<-lapply(direct, function(x) read.table(x,header=TRUE, sep =
"\t"))
>names(lista)<-filelist
>return(lista)
>}
>filelist(directory,23)
>
>
>###"a1" "a2" "c1" "c2"
"c3" "t1" "t2"
>
>
>
>and after
>
>f<-function(filelist,FacGroup){
>
>res2<-split(lista,names(lista))
>?res3<- lapply(res2,function(x)
{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
>res3
>#Freq FDR<0.01
>?res4<-lapply(seq_along(res3),function(i) lapply(res3[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
>?names(res4)<- names(res2)
>?res4
>? res4New<-lapply(res4,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x))) ))
>?res5<- lapply(res4New,function(x) if(length(x)>1) tail(x,-1) else
NULL)
>?library(plyr)
>?library(data.table)
>?res6<- lapply(res5,function(x) lapply(x,function(x1)
{x1<-data.table(x1); x1[,spec:=past
>
>
>
>
>How can I "ask lista in second function? Could you help
me??????????????
>????

arun

2013-Mar-16 03:09 UTC

head link

[R] new question

Hi,
Try this:

directory<- "/home/arunksa111/dados" 
#modified the function
GetFileList <- function(directory,number){
?setwd(directory)
?filelist1<-dir()
??? lista<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = TRUE, recursive = TRUE)
???? output<- list(filelist1,lista)
?return(output)
??? }

?file.list.names<-GetFileList(directory,23)[[1]]
?lista<-GetFileList(directory,23)[[2]]
FacGroup<-c(0,1,0,2,2,0,3)


ReadDir<-function(FacGroup){
?list.new<-lista[FacGroup!=0]
?read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
?names(read.list)<-file.list.names[FacGroup!=0]
?return (read.list)
} 
ListFacGroup<-ReadDir(FacGroup)

z.boxplot<- function(lst){
new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
pdf("VeraBP.pdf")
lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
dev.off()
}
z.boxplot(ListFacGroup)

A.K.

________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Friday, March 15, 2013 2:08 PM
Subject: Re: new question


Sorry, you could give me a small new help?

Using the same data, I need a boxplot by groups.

I write he the functions I'm using. The last (z.boxplot is what I need, the
other is ok). Thank you one more time.

GetFileList <- function(directory,number){
?setwd(directory)
?filelist1<-dir()[file.info(dir())$isdir]
??? direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
?direct<-lapply(direct,function(x)
paste(directory,"/",x,sep=""))
??? lista<-unlist(direct)
?output<- list(filelist1,lista)
?return(output)
??? }

ReadDir<-function(FacGroup){
?list.new<-lista[FacGroup!=0]
?read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
?names(read.list)<-file.list.names[FacGroup!=0]
?return (read.list)
} 

directory<-"C:/Users/Vera Costa/Desktop/dados.lixo"
?file.list.names<-GetFileList(directory,23) [[1]]
?lista<-GetFileList(directory,23) [[2]]
FacGroup<-c(0,1,0,2,2,0,3)
ListFacGroup<-ReadDir(FacGroup)
#zPValues(ListFacGroup,FacGroup) 

z.boxplot <- function(lista) {
#I need eliminate all data with FDR<0.01
new.list<-lista[FDR<0.01]
#boxplots split by groups?
boxplot(FDR ~ z, data = dct1,? xlab = "Charge", ylab =
"FDR",main=(paste("t",i)))
?}
z.boxplot(ListFacGroup)




2013/3/13 Vera Costa <veracosta.rt at gmail.com>

No problem!>Sorry my questions.
>
>
>
>2013/3/13 arun <smartpink111 at yahoo.com>
>
>As I mentioned earlier, I don't find it useful to do anova on that kind
of data.? Previously, I tried with chisq.test also.? It gave warnings() and then
you responded that it is not correct.? I would suggest you to dput an example
dataset of the specific columns? that you want to compare (possibly by row) and
post in the R-help list.? If you get any reply, then you can implement it on
your whole list of files.? Sorry, today, I am busy. ? ?
>>
>>
>>
>>
>>
>>
>>
>>________________________________
>>From: Vera Costa <veracosta.rt at gmail.com>
>>To: arun <smartpink111 at yahoo.com>
>>Sent: Wednesday, March 13, 2013 9:43 AM
>>
>>Subject: Re: new question
>>
>>
>>Ok. Thank you.
>>Could you help me to apply this?
>>
>>
>>
>>2013/3/13 arun <smartpink111 at yahoo.com>
>>
>>you are comparing one datapoint to another.? It doesn't make sense.?
For anova, you need replications to calculate df.? may be you could try
chisq.test.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>________________________________
>>>From: Vera Costa <veracosta.rt at gmail.com>
>>>To: arun <smartpink111 at yahoo.com>
>>>Sent: Wednesday, March 13, 2013 8:56 AM
>>>
>>>Subject: Re: new question
>>>
>>>
>>>I agree with you.
>>>
>>>I write this tests because I need to compare with some test. I agree
is not very correct, but what is bioconductor?I need to eliminate some data
(rows) not very significant based in some statistics. What about your idea? How
can I do this?
>>>
>>>
>>>
>>>2013/3/13 arun <smartpink111 at yahoo.com>
>>>
>>>Ok.
>>>>
>>>>"
>>>>
>>>>I need a t test (it's in this function). But I need a
chisq.test corrected and a Anova with data in attach.
>>>>"
>>>>What do you mean by this?
>>>>
>>>>Though, I calculated the t test based on comparing a single
value against another for each row, I don't think it makes sense
statistically.? Here, you are estimating the mean by just one value, which then
is the mean value and comparing it with another value.? It doesn't make much
sense.? I think in bioconductor there are some packages which do this kind of
comparison (I don't remember the names).? Also, I am not sure what kind of
inference you want from chisquare test.? Also, from anova test (?using just 2
datapoints) (if the comparison is rowwise).
>>>>
>>>>
>>>>
>>>>
>>>>________________________________
>>>>From: Vera Costa <veracosta.rt at gmail.com>
>>>>To: arun <smartpink111 at yahoo.com>
>>>>Sent: Tuesday, March 12, 2013 6:04 PM
>>>>
>>>>Subject: Re: new question
>>>>
>>>>
>>>>Ok. It isn't the last code...
>>>>You sent me this code
>>>>
>>>>directory<- "/home/arunksa111/data.new"
>>>>#first function
>>>>filelist<-function(directory,number,list1){
>>>>setwd(directory)
>>>>filelist1<-dir(directory)
>>>>
>>>>direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
>>>>
>>>>list1<-lapply(direct, function(x) read.table(x,header=TRUE,
sep = "\t",stringsAsFactors=FALSE))
>>>>names(list1)<-filelist1
>>>>list2<- list(filelist1,list1)
>>>>return(list2)
>>>>}
>>>>foldernames1<-filelist(directory,23,list1)[[1]]
>>>>foldernames1
>>>>#[1] "a1" "c1" "c2" "c3"
"t1" "t2"
>>>>lista<-filelist(directory,23,list1)[[2]] #lista output
>>>>
>>>>FacGroup<- c("c1","c3","t2")
>>>>
>>>>#Second function
>>>>f<-function(listRes,Toselect){
>>>>res2<-split(listRes,gsub("[0-9]","",names(listRes)))
>>>>res3<-lapply(seq_along(res2),function(i)
lapply(res2[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
>>>>res4<-lapply(res3,function(x)
x[names(x)[names(x)%in%Toselect]])
>>>>res4New<- lapply(res4,function(x) lapply(names(x),
function(i) do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x))) ))
>>>>library(plyr)
>>>>library(data.table)
>>>>res5<-lapply(res4New,function(x) lapply(x,function(x1){
x1<-
data.table(x1);x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))
>>>>res6<- lapply(res5,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
>>>>
>>>>res7<-lapply(res6,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
>>>>?res8<-res7[lapply(res7,length)!=0]
>>>>?res9<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),res8)
>>>>res9[is.na(res9)] <- 0
>>>>return(res9)
>>>>}
>>>>
>>>>f(lista,FacGroup)
>>>>?head(f(lista,FacGroup))
>>>>?#??????????????????? Seq??????? Mod z c1 c3 t2
>>>>#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 0? 0? 1
>>>>#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 0? 0? 1
>>>>#3?????? aAAAAAAAAAGAAGGR 1-n_acPro/ 2? 0? 0? 1
>>>>#4? aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2? 1? 0? 0
>>>>#5??????????? AAAAAAALQAK??????????? 2? 0? 1? 1
>>>>#6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2
>>>>
>>>>resCounts<- f(lista,FacGroup)
>>>>t.test.p.value <- function(...) {
>>>>??? obj<-try(t.test(...), silent=TRUE)
>>>>??? if (is(obj, "try-error")) return(NA) else
return(obj$p.value)
>>>>?}
>>>>
>>>>#3rd function for p-value
>>>>fpv<- function(Countdata){
>>>>resNew<-do.call(cbind,lapply(split(names(Countdata)[4:ncol(Countdata)],gsub("[0-9]","",names(Countdata)[4:ncol(Countdata)])),
function(i) {x<-if(ncol(Countdata[i])>1) rowSums(Countdata[i]) else
Countdata[i]; colnames(x)<-NULL;x}))
>>>>indx<-combn(names(resNew),2)
>>>>resPval<-do.call(cbind,lapply(seq_len(ncol(indx)),function(i)
{x<-as.data.frame(apply(resNew[,indx[,i]],1,t.test.p.value));
colnames(x)<-paste("Pvalue",paste(indx[,i],collapse=""),sep="_");x}))
>>>>resF<-cbind(resCounts,resPval)
>>>>resF
>>>>}
>>>>
>>>>fpv(resCounts)
>>>>
>>>>
>>>>I need a t test (it's in this function). But I need a
chisq.test corrected and a Anova with data in attach.
>>>>Sorry!
>>>>
>>>>
>>>>No dia 12 de Mar de 2013 20:08, "arun"
<smartpink111 at yahoo.com> escreveu:
>>>>
>>>>where is the reference "t-test above"?
>>>>>
>>>>>Which dataset you want to do this?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>________________________________
>>>>>From: Vera Costa <veracosta.rt at gmail.com>
>>>>>To: arun <smartpink111 at yahoo.com>
>>>>>Sent: Tuesday, March 12, 2013 1:50 PM
>>>>>Subject: Re: new question
>>>>>
>>>>>
>>>>>Hi.
>>>>>
>>>>>Could I ask a little help?
>>>>>
>>>>>Could you hel me to do a chisq.test (corrected), and a
Anova, like a t-test above? After that I need to remove all data with a p
values<0.05.
>>>>>
>>>>>Sorry and thank you again
>>>>>
>>>>>
>>>>>
>>>>>2013/3/7 arun <smartpink111 at yahoo.com>
>>>>>
>>>>>Hi,
>>>>>>
>>>>>>
>>>>>>directory<- "/home/arunksa111/dados"
#renamed directory to dados
>>>>>>
>>>>>>filelist<-function(directory,number,list1){
>>>>>>setwd(directory)
>>>>>>filelist1<-dir(directory)
>>>>>>direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
>>>>>>list1<-lapply(direct, function(x)
read.table(x,header=TRUE, sep = "\t",stringsAsFactors=FALSE))
>>>>>>names(list1)<-filelist1
>>>>>>list2<- list(filelist1,list1)
>>>>>>return(list2)
>>>>>>}
>>>>>>foldernames1<-filelist(directory,23,list1)[[1]]
>>>>>>foldernames1
>>>>>>#[1] "a1" "a2" "c1"
"c2" "c3" "t1" "t2"
>>>>>>
>>>>>>lista<-filelist(directory,23,list1)[[2]] #lista
output?
>>>>>>
>>>>>>#If you look at the
>>>>>>?lapply(lista,function(x) sapply(x,class)) #some spec
were integer, and some were character
>>>>>>#do this
>>>>>>?listaNew<-lapply(lista,function(x)
within(x,{spec<- as.character(spec)}))
>>>>>>
>>>>>>
>>>>>>FacGroup<-
c("c1","c3","t2")
>>>>>>#Second function
>>>>>>#f<- function(....)
>>>>>>
>>>>>>head(f(listaNew,FacGroup))
>>>>>>
>>>>>>#???????????????????? Seq??????? Mod z c1 c3 t2
>>>>>>#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 0? 0? 1
>>>>>>#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 0? 0? 1
>>>>>>#3?????? aAAAAAAAAAGAAGGR 1-n_acPro/ 2? 0? 0? 1
>>>>>>#4? aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2? 1? 0? 0
>>>>>>#5??????????? AAAAAAALQAK??????????? 2? 0? 1? 1
>>>>>>#6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2
>>>>>>
>>>>>>
>>>>>>
>>>>>>A.K.
>>>>>>
>>>>>>
>>>>>>
>>>>>>________________________________
>>>>>>From: Vera Costa <veracosta.rt at gmail.com>
>>>>>>To: arun <smartpink111 at yahoo.com>
>>>>>>
>>>>>>Sent: Thursday, March 7, 2013 7:12 AM
>>>>>>Subject: Re: new question
>>>>>>
>>>>>>
>>>>>>
>>>>>>Hi.
>>>>>>
>>>>>>Sorry again a question about this, but when I run this
code I have this error:
>>>>>>
>>>>>>Error in `[.data.table`(x1, , `:=`(spec, paste(spec,
collapse = ",")),? :
>>>>>>? Type of RHS ('character') must match LHS
('integer'). To check and coerce would impact performance too much for
the fastest cases. Either change the type of the target column, or coerce the
RHS of := yourself (e.g. by using 1L instead of 1)
>>>>>>
>>>>>>Could you help me to with this? How can I eliminate
this?
>>>>>>
>>>>>>Thank you
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>2013/2/28 arun <smartpink111 at yahoo.com>
>>>>>>
>>>>>>Hi,
>>>>>>>directory<- "/home/arunksa111/data.new"
>>>>>>>#first function
>>>>>>>filelist<-function(directory,number,list1){
>>>>>>>setwd(directory)
>>>>>>>filelist1<-dir(directory)
>>>>>>>
>>>>>>>direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
>>>>>>>list1<-lapply(direct, function(x)
read.table(x,header=TRUE, sep = "\t",stringsAsFactors=FALSE))
>>>>>>>names(list1)<-filelist1
>>>>>>>list2<- list(filelist1,list1)
>>>>>>>return(list2)
>>>>>>>}
>>>>>>>foldernames1<-filelist(directory,23,list1)[[1]]
>>>>>>>foldernames1
>>>>>>>#[1] "a1" "c1" "c2"
"c3" "t1" "t2"
>>>>>>>lista<-filelist(directory,23,list1)[[2]] #lista
output
>>>>>>>
>>>>>>>FacGroup<-
c("c1","c3","t2")
>>>>>>>
>>>>>>>#Second function
>>>>>>>f<-function(listRes,Toselect){
>>>>>>>res2<-split(listRes,gsub("[0-9]","",names(listRes)))
>>>>>>>res3<-lapply(seq_along(res2),function(i)
lapply(res2[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
>>>>>>>res4<-lapply(res3,function(x)
x[names(x)[names(x)%in%Toselect]])
>>>>>>>res4New<- lapply(res4,function(x)
lapply(names(x), function(i) do.call(rbind,lapply(x[i],function(x)
cbind(folder_name=i,x))) ))
>>>>>>>library(plyr)
>>>>>>>library(data.table)
>>>>>>>res5<-lapply(res4New,function(x)
lapply(x,function(x1){ x1<-
data.table(x1);x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))
>>>>>>>res6<- lapply(res5,function(x)
lapply(x,function(x1) {x1$counts<-sapply(x1$spec, function(x2)
length(gsub("\\s", "", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
>>>>>>>?
>>>>>>>res7<-lapply(res6,function(x)
Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
>>>>>>>?res8<-res7[lapply(res7,length)!=0]
>>>>>>>?res9<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),res8)
>>>>>>>res9[is.na(res9)] <- 0
>>>>>>>return(res9)
>>>>>>>}
>>>>>>>
>>>>>>>f(lista,FacGroup)
>>>>>>>?head(f(lista,FacGroup))
>>>>>>>?#??????????????????? Seq??????? Mod z c1 c3 t2
>>>>>>>#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 0? 0? 1
>>>>>>>#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 0? 0? 1
>>>>>>>#3?????? aAAAAAAAAAGAAGGR 1-n_acPro/ 2? 0? 0? 1
>>>>>>>#4? aAAAAAAAGAAGGRGSGPGRR 1-n_acPro/ 2? 1? 0? 0
>>>>>>>#5??????????? AAAAAAALQAK??????????? 2? 0? 1? 1
>>>>>>>#6???????? aAAAAAGAGPEMVR 1-n_acPro/ 2? 0? 0? 2
>>>>>>>
>>>>>>>resCounts<- f(lista,FacGroup)
>>>>>>>t.test.p.value <- function(...) {
>>>>>>>??? obj<-try(t.test(...), silent=TRUE)
>>>>>>>??? if (is(obj, "try-error")) return(NA)
else return(obj$p.value)
>>>>>>>?}
>>>>>>>
>>>>>>>#3rd function for p-value
>>>>>>>fpv<- function(Countdata){
>>>>>>>resNew<-do.call(cbind,lapply(split(names(Countdata)[4:ncol(Countdata)],gsub("[0-9]","",names(Countdata)[4:ncol(Countdata)])),
function(i) {x<-if(ncol(Countdata[i])>1) rowSums(Countdata[i]) else
Countdata[i]; colnames(x)<-NULL;x}))
>>>>>>>indx<-combn(names(resNew),2)
>>>>>>>resPval<-do.call(cbind,lapply(seq_len(ncol(indx)),function(i)
{x<-as.data.frame(apply(resNew[,indx[,i]],1,t.test.p.value));
colnames(x)<-paste("Pvalue",paste(indx[,i],collapse=""),sep="_");x}))
>>>>>>>resF<-cbind(resCounts,resPval)
>>>>>>>resF
>>>>>>>}
>>>>>>>
>>>>>>>fpv(resCounts)
>>>>>>>
>>>>>>>
>>>>>>>A.K.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>________________________________
>>>>>>>From: Vera Costa <veracosta.rt at gmail.com>
>>>>>>>To: arun <smartpink111 at yahoo.com>
>>>>>>>Sent: Thursday, February 28, 2013 11:30 AM
>>>>>>>Subject: new question
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>Sorry about my question, but I need a new small
thing...I need to split my function to read data and to do the treatment of the
data.
>>>>>>>
>>>>>>>At first I need to know the "names" of the
files and read data, and after a new function with my analysis.
>>>>>>>
>>>>>>>So, I did this
>>>>>>>
>>>>>>>directory<-"C:/Users/Vera
Costa/Desktop/data.new"?
>>>>>>>filelist<-function(directory,number){
>>>>>>>setwd(directory)
>>>>>>>filelist<-dir(directory)
>>>>>>>return(filelist)
>>>>>>>direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
>>>>>>>lista<-lapply(direct, function(x)
read.table(x,header=TRUE, sep = "\t"))
>>>>>>>names(lista)<-filelist
>>>>>>>return(lista)
>>>>>>>}
>>>>>>>filelist(directory,23)
>>>>>>>
>>>>>>>
>>>>>>>###"a1" "a2" "c1"
"c2" "c3" "t1" "t2"
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>and after
>>>>>>>
>>>>>>>f<-function(filelist,FacGroup){
>>>>>>>
>>>>>>>res2<-split(lista,names(lista))
>>>>>>>?res3<- lapply(res2,function(x)
{names(x)<-paste(gsub(".*_","",names(x)),1:length(x),sep="");x})
>>>>>>>res3
>>>>>>>#Freq FDR<0.01
>>>>>>>?res4<-lapply(seq_along(res3),function(i)
lapply(res3[[i]],function(x)
x[x[["FDR"]]<0.01,c("Seq","Mod","z","spec")]))
>>>>>>>?names(res4)<- names(res2)
>>>>>>>?res4
>>>>>>>? res4New<-lapply(res4,function(x)
lapply(names(x),function(i) do.call(rbind,lapply(x[i],function(x)
cbind(folder_name=i,x))) ))
>>>>>>>?res5<- lapply(res4New,function(x)
if(length(x)>1) tail(x,-1) else NULL)
>>>>>>>?library(plyr)
>>>>>>>?library(data.table)
>>>>>>>?res6<- lapply(res5,function(x)
lapply(x,function(x1) {x1<-data.table(x1); x1[,spec:=past
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>How can I "ask lista in second function? Could
you help me??????????????
>>>>>>>????
>>>>>>???
>>>>>??????
>>>>?
>>>
>>
>?????-------------- next part --------------
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arun

2013-Mar-18 18:27 UTC

head link

[R] new question

?z.boxplot<- function(lst){
?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
print(new.list)
? par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))

}
?z.boxplot(ListFacGroup) #prints new.list

If you want to turn off that:
?z.boxplot<- function(lst){
?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
#print(new.list)
? par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))

}
?z.boxplot(ListFacGroup)
A.K.





________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Monday, March 18, 2013 1:59 PM
Subject: Re: new question


For example, if I run you code without "pdf...." and
"dev.off" I have what I want

directory<- "C:/Users/Vera Costa/Desktop/dados.lixo"
?#modified the function
GetFileList <- function(directory,number){
? setwd(directory)
? filelist1<-dir()

??? lista<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = TRUE, recursive = TRUE)
????? output<- list(filelist1,lista)
? return(output)
???? }
file.list.names<-GetFileList(directory,23)[[1]]
lista<-GetFileList(directory,23)[[2]]
FacGroup<-c(0,1,0,2,2,0,3)
ReadDir<-function(FacGroup){
? list.new<-lista[FacGroup!=0]
? read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
? names(read.list)<-file.list.names[FacGroup!=0]
? return (read.list)
?}
ListFacGroup<-ReadDir(FacGroup)
ListFacGroup
?z.boxplot<- function(lst){
?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
?print(new.list)
?#pdf("VeraBP.pdf")
?par(mfrow=c(2,2))
?lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
?#dev.off()
?}
?z.boxplot(ListFacGroup)





But I have the results too (I don't need it)


[[1]]
[[1]]$a2
[[1]]$a2$stats
???????????? [,1]???????? [,2]
[1,] 0.0000000000 0.0000000000
[2,] 0.0000000000 0.0000000000
[3,] 0.0001355197 0.0002175095
[4,] 0.0010588777 0.0004350190
[5,] 0.0016571381 0.0004350190
[[1]]$a2$n
[1] 8 2
[[1]]$a2$conf
????????????? [,1]????????? [,2]
[1,] -0.0004559846 -0.0002685062
[2,]? 0.0007270240? 0.0007035253
[[1]]$a2$out
[1] 0.00494012
[[1]]$a2$group
[1] 1
[[1]]$a2$names
[1] "2" "3"

[[2]]
[[2]]$c2
[[2]]$c2$stats
???????????? [,1]???????? [,2]
[1,] 0.0000000000 0.0000000000
[2,] 0.0000000000 0.0000000000
[3,] 0.0001355197 0.0002175095
[4,] 0.0010588777 0.0004350190
[5,] 0.0016571381 0.0004350190
[[2]]$c2$n
[1] 8 2
[[2]]$c2$conf
????????????? [,1]????????? [,2]
[1,] -0.0004559846 -0.0002685062
[2,]? 0.0007270240? 0.0007035253
[[2]]$c2$out
[1] 0.00494012
[[2]]$c2$group
[1] 1
[[2]]$c2$names
[1] "2" "3"

[[3]]
[[3]]$c3
[[3]]$c3$stats
??????????? [,1]???????? [,2]
[1,] 0.000000000 0.0000000000
[2,] 0.000000000 0.0000000000
[3,] 0.000000000 0.0000000000
[4,] 0.002226409 0.0002086594
[5,] 0.002226409 0.0004173187
[[3]]$c3$n
[1] 6 4
[[3]]$c3$conf
???????????? [,1]????????? [,2]
[1,] -0.001436105 -0.0001648409
[2,]? 0.001436105? 0.0001648409
[[3]]$c3$out
[1] 0.00560348
[[3]]$c3$group
[1] 1
[[3]]$c3$names
[1] "2" "3"

[[4]]
[[4]]$t2
[[4]]$t2$stats
???? [,1]???????? [,2] [,3]
[1,]??? 0 0.0000000000??? 0
[2,]??? 0 0.0000000000??? 0
[3,]??? 0 0.0002908668??? 0
[4,]??? 0 0.0025929827??? 0
[5,]??? 0 0.0052577771??? 0
[[4]]$t2$n
[1]? 1 10? 5
[[4]]$t2$conf
???? [,1]???????? [,2] [,3]
[1,]??? 0 -0.001004691??? 0
[2,]??? 0? 0.001586424??? 0
[[4]]$t2$out
[1] 0.0092051934 0.0007174888
[[4]]$t2$group
[1] 2 3
[[4]]$t2$names
[1] "1" "2" "3"

arun

2013-Mar-19 16:40 UTC

head link

[R] new question

I deleted the 't' subfolders from the dados folder.

If you don't have 't' folders, wouldn't it be better to use:
directory<- "/home/arunksa111/dados"


FacGroup<-c(0,1,0,2,2,0,0)
#instead of

#FacGroup<-c(0,1,0,2,2,0,3)
FacGroup<-c(0,1,0,2,2,0,3)
?lista[FacGroup!=0]
#[1] "/home/arunksa111/dados/a2/MSMS_23PepInfo.txt"
#[2] "/home/arunksa111/dados/c2/MSMS_23PepInfo.txt"
#[3] "/home/arunksa111/dados/c3/MSMS_23PepInfo.txt"
#[4] NA???????? 

FacGroup<-c(0,1,0,2,2,0,0)
?lista[FacGroup!=0]
#[1] "/home/arunksa111/dados/a2/MSMS_23PepInfo.txt"
#[2] "/home/arunksa111/dados/c2/MSMS_23PepInfo.txt"
#[3] "/home/arunksa111/dados/c3/MSMS_23PepInfo.txt"


Couldn't reproduce the error you mentioned.

Spec(ListFacGroup,0.05)
#?????????????????????????????? Seq???????????????? Mod z a2 c2 c3
#1???????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0
#2????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 1? 1? 0
#3?????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1
#4??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 1? 1? 0
#5??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 2? 2? 2
#6????????????????????? AAAAAPGTAEK???????????????????? 2? 1? 1? 0
#7????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1
_______________________________________________________
-----------------------------------------------------------------------------------------
A.K.




________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Tuesday, March 19, 2013 10:14 AM
Subject: Re: new question


Hi again. 

you sent me a code ( e few time ago)

GetFileList <- function(directory,number){
?setwd(directory)
?filelist1<-dir()[file.info(dir())$isdir]
??? direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
?direct<-lapply(direct,function(x)
paste(directory,"/",x,sep=""))
??? lista<-unlist(direct)
?output<- list(filelist1,lista)
?return(output)
??? }

ReadDir<-function(FacGroup){
?list.new<-lista[FacGroup!=0]
?read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
?names(read.list)<-file.list.names[FacGroup!=0]
?return (read.list)
} 

directory<-"C:/Users/Vera Costa/Desktop/dados.lixo"
?file.list.names<-GetFileList(directory,23) [[1]]
?lista<-GetFileList(directory,23) [[2]]
FacGroup<-c(0,1,0,2,2,0,3)
#FacGroup<-c(0,1,1,1,0,2,2,2)
ListFacGroup<-ReadDir(FacGroup)
#zPValues(ListFacGroup,FacGroup) 

?Spec <- function(lista,FDR_k) {

?list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
?split.list<-split(list.new,names(lista))

?#Data needed with FDR<FDR_k
?seq.mod.z<-lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x)
x[x[["FDR"]]<FDR_k,c("Seq","Mod","z","spec")]))
?names(seq.mod.z)<- names(split.list)?

?#insert colunm with the name of the folder 
?folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
?#merge data with the same Seq, Mod and z
?library(plyr)
?library(data.table)
?merge.data<- lapply(folder.name,function(x) lapply(x,function(x1)
{x1<-data.table(x1);
x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))

?#colunm with number of spec
?count.spec<-lapply(merge.data,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))

?#count spec by group (2-columns)
?spec.group<-lapply(count.spec,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
??#spec.group1<-spec.group[lapply(spec.group,length)!=0]

?#data frame with count of spec
?res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),spec.group)
?res[is.na(res)] <- 0
?print(res)
?resNew<-do.call(cbind,lapply(split(names(res)[4:ncol(res)],gsub("[0-9]","",names(res)[4:ncol(res)])),
function(i) {x<-if(ncol(res[i])>1) rowSums(res[i]) else res[i];
colnames(x)<-NULL;x}))
?print(head(resNew),10)
?print("vera")
?print(names(resNew))
?indx<-combn(names(resNew),2)
??t.test.p.value <- function(...) {
??obj<-try(t.test(...), silent=TRUE)
??if (is(obj, "try-error")) return(NA) else return(obj$p.value)
??}

?resPval<-do.call(cbind,lapply(seq_len(ncol(indx)),function(i)
{x<-as.data.frame(apply(resNew[,indx[,i]],1,t.test.p.value));
colnames(x)<-paste("Pvalue",paste(indx[,i],collapse=""),sep="_");x}))
?print(resPval)
?resF<-cbind(res,resPval)
?print(resF)

Spec(ListFacGroup,0.05) 



And it is ok for the file list that you have. But if I apply to one file list
with only a and c (for example) I have an error "Error in
combn(names(resNew), 2) : n < m" How can I adapt this for all cases?



2013/3/18 arun <smartpink111 at yahoo.com>

I hope this solved the problem...>
>
>
>
>----- Original Message -----
>From: arun <smartpink111 at yahoo.com>
>To: Vera Costa <veracosta.rt at gmail.com>
>Cc: R help <r-help at r-project.org>
>
>Sent: Monday, March 18, 2013 2:27 PM
>Subject: Re: new question
>
>
>
>
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>print(new.list)
>? par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>}
>?z.boxplot(ListFacGroup) #prints new.list
>
>If you want to turn off that:
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>#print(new.list)
>? par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>}
>?z.boxplot(ListFacGroup)
>A.K.
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta.rt at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Monday, March 18, 2013 1:59 PM
>Subject: Re: new question
>
>
>For example, if I run you code without "pdf...." and
"dev.off" I have what I want
>
>directory<- "C:/Users/Vera Costa/Desktop/dados.lixo"
>?#modified the function
>GetFileList <- function(directory,number){
>? setwd(directory)
>? filelist1<-dir()
>
>??? lista<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = TRUE, recursive = TRUE)
>????? output<- list(filelist1,lista)
>? return(output)
>???? }
>file.list.names<-GetFileList(directory,23)[[1]]
>lista<-GetFileList(directory,23)[[2]]
>FacGroup<-c(0,1,0,2,2,0,3)
>ReadDir<-function(FacGroup){
>? list.new<-lista[FacGroup!=0]
>? read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
>? names(read.list)<-file.list.names[FacGroup!=0]
>? return (read.list)
>?}
>ListFacGroup<-ReadDir(FacGroup)
>ListFacGroup
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>?print(new.list)
>?#pdf("VeraBP.pdf")
>?par(mfrow=c(2,2))
>?lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>?#dev.off()
>?}
>?z.boxplot(ListFacGroup)
>
>
>
>
>
>But I have the results too (I don't need it)
>
>
>[[1]]
>[[1]]$a2
>[[1]]$a2$stats
>???????????? [,1]???????? [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[1]]$a2$n
>[1] 8 2
>[[1]]$a2$conf
>????????????? [,1]????????? [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,]? 0.0007270240? 0.0007035253
>[[1]]$a2$out
>[1] 0.00494012
>[[1]]$a2$group
>[1] 1
>[[1]]$a2$names
>[1] "2" "3"
>
>[[2]]
>[[2]]$c2
>[[2]]$c2$stats
>???????????? [,1]???????? [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[2]]$c2$n
>[1] 8 2
>[[2]]$c2$conf
>????????????? [,1]????????? [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,]? 0.0007270240? 0.0007035253
>[[2]]$c2$out
>[1] 0.00494012
>[[2]]$c2$group
>[1] 1
>[[2]]$c2$names
>[1] "2" "3"
>
>[[3]]
>[[3]]$c3
>[[3]]$c3$stats
>??????????? [,1]???????? [,2]
>[1,] 0.000000000 0.0000000000
>[2,] 0.000000000 0.0000000000
>[3,] 0.000000000 0.0000000000
>[4,] 0.002226409 0.0002086594
>[5,] 0.002226409 0.0004173187
>[[3]]$c3$n
>[1] 6 4
>[[3]]$c3$conf
>???????????? [,1]????????? [,2]
>[1,] -0.001436105 -0.0001648409
>[2,]? 0.001436105? 0.0001648409
>[[3]]$c3$out
>[1] 0.00560348
>[[3]]$c3$group
>[1] 1
>[[3]]$c3$names
>[1] "2" "3"
>
>[[4]]
>[[4]]$t2
>[[4]]$t2$stats
>???? [,1]???????? [,2] [,3]
>[1,]??? 0 0.0000000000??? 0
>[2,]??? 0 0.0000000000??? 0
>[3,]??? 0 0.0002908668??? 0
>[4,]??? 0 0.0025929827??? 0
>[5,]??? 0 0.0052577771??? 0
>[[4]]$t2$n
>[1]? 1 10? 5
>[[4]]$t2$conf
>???? [,1]???????? [,2] [,3]
>[1,]??? 0 -0.001004691??? 0
>[2,]??? 0? 0.001586424??? 0
>[[4]]$t2$out
>[1] 0.0092051934 0.0007174888
>[[4]]$t2$group
>[1] 2 3
>[[4]]$t2$names
>[1] "1" "2" "3"
>
>???????????? ???

arun

2013-Mar-21 15:29 UTC

head link

[R] new question

Sorry, I am not sure I understand your question.? 

You have 5 boxplots(if I remember correctly) on a single page and these 5
boxplots have titles
"a1","a2","c1","c2","t1" (or
something like that).

Could you try:
par(mfcol(c(3,2)) and see if that helps. (not tested)
A.K.






________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 21, 2013 11:24 AM
Subject: Re: new question


Hi.

Thank you your help and sorry only answer now. 

Ok, the boxplots is ok. But I need too by group... on par(mfrow(c(2,2))), I can
have par(mfrow(c(3,2)), for example (or more) and have a boxplot for the group.
You can help me to group them?

About the other function I need to do other things, but now I need to think what
to do...

Thank you





2013/3/18 arun <smartpink111 at yahoo.com>

>
>
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>print(new.list)
>? par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>}
>?z.boxplot(ListFacGroup) #prints new.list
>
>If you want to turn off that:
>
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>#print(new.list)
>? par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>
>}
>?z.boxplot(ListFacGroup)
>A.K.
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta.rt at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Monday, March 18, 2013 1:59 PM
>Subject: Re: new question
>
>
>
>For example, if I run you code without "pdf...." and
"dev.off" I have what I want
>
>directory<- "C:/Users/Vera Costa/Desktop/dados.lixo"
>?#modified the function
>GetFileList <- function(directory,number){
>? setwd(directory)
>? filelist1<-dir()
>
>??? lista<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = TRUE, recursive = TRUE)
>????? output<- list(filelist1,lista)
>? return(output)
>???? }
>file.list.names<-GetFileList(directory,23)[[1]]
>lista<-GetFileList(directory,23)[[2]]
>FacGroup<-c(0,1,0,2,2,0,3)
>ReadDir<-function(FacGroup){
>? list.new<-lista[FacGroup!=0]
>? read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
>? names(read.list)<-file.list.names[FacGroup!=0]
>? return (read.list)
>?}
>ListFacGroup<-ReadDir(FacGroup)
>ListFacGroup
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>?print(new.list)
>?#pdf("VeraBP.pdf")
>?par(mfrow=c(2,2))
>?lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>?#dev.off()
>?}
>?z.boxplot(ListFacGroup)
>
>
>
>
>
>But I have the results too (I don't need it)
>
>
>[[1]]
>[[1]]$a2
>[[1]]$a2$stats
>???????????? [,1]???????? [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[1]]$a2$n
>[1] 8 2
>[[1]]$a2$conf
>????????????? [,1]????????? [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,]? 0.0007270240? 0.0007035253
>[[1]]$a2$out
>[1] 0.00494012
>[[1]]$a2$group
>[1] 1
>[[1]]$a2$names
>[1] "2" "3"
>
>[[2]]
>[[2]]$c2
>[[2]]$c2$stats
>???????????? [,1]???????? [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[2]]$c2$n
>[1] 8 2
>[[2]]$c2$conf
>????????????? [,1]????????? [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,]? 0.0007270240? 0.0007035253
>[[2]]$c2$out
>[1] 0.00494012
>[[2]]$c2$group
>[1] 1
>[[2]]$c2$names
>[1] "2" "3"
>
>[[3]]
>[[3]]$c3
>[[3]]$c3$stats
>??????????? [,1]???????? [,2]
>[1,] 0.000000000 0.0000000000
>[2,] 0.000000000 0.0000000000
>[3,] 0.000000000 0.0000000000
>[4,] 0.002226409 0.0002086594
>[5,] 0.002226409 0.0004173187
>[[3]]$c3$n
>[1] 6 4
>[[3]]$c3$conf
>???????????? [,1]????????? [,2]
>[1,] -0.001436105 -0.0001648409
>[2,]? 0.001436105? 0.0001648409
>[[3]]$c3$out
>[1] 0.00560348
>[[3]]$c3$group
>[1] 1
>[[3]]$c3$names
>[1] "2" "3"
>
>[[4]]
>[[4]]$t2
>[[4]]$t2$stats
>???? [,1]???????? [,2] [,3]
>[1,]??? 0 0.0000000000??? 0
>[2,]??? 0 0.0000000000??? 0
>[3,]??? 0 0.0002908668??? 0
>[4,]??? 0 0.0025929827??? 0
>[5,]??? 0 0.0052577771??? 0
>[[4]]$t2$n
>[1]? 1 10? 5
>[[4]]$t2$conf
>???? [,1]???????? [,2] [,3]
>[1,]??? 0 -0.001004691??? 0
>[2,]??? 0? 0.001586424??? 0
>[[4]]$t2$out
>[1] 0.0092051934 0.0007174888
>[[4]]$t2$group
>[1] 2 3
>[[4]]$t2$names
>[1] "1" "2" "3"
>??????

arun

2013-Mar-21 17:21 UTC

head link

[R] new question

Hi,
Try this:


directory<- "/home/arunksa111/dados"
GetFileList <- function(directory,number){
?setwd(directory)
?filelist1<-dir()[file.info(dir())$isdir]
??? direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
?direct<-lapply(direct,function(x)
paste(directory,"/",x,sep=""))
??? lista<-unlist(direct)
?output<- list(filelist1,lista)
?return(output)
??? }

?file.list.names<-GetFileList(directory,23)[[1]]
?lista<-GetFileList(directory,23)[[2]]
FacGroup<-c(0,1,0,2,2,0,3)


ReadDir<-function(FacGroup){
?list.new<-lista[FacGroup!=0]
?read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
?names(read.list)<-file.list.names[FacGroup!=0]
?return (read.list)
}
ListFacGroup<-ReadDir(FacGroup)

z.boxplotgroup<- function(lst){
lst1<- lapply(lst,function(x) x[x$FDR<0.01,])
library(plyr)
new.list<-lapply(split(lst1,gsub("\\d+","",names(lst1))),function(x)
join_all(lapply(x,function(x) x),type="full"))
par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
}

z.boxplotgroup(ListFacGroup)

z.boxplot<- function(lst){
?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
#print(new.list)
? par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
}
?z.boxplot(ListFacGroup)


?pdf("Veraboxplot.pdf")
?z.boxplot(ListFacGroup)
?z.boxplotgroup(ListFacGroup)
Joining by: Seq, Mod, z, score, FDR, Count, E, C, pos, spec, Pro
?dev.off()
A.K.


________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 21, 2013 11:24 AM
Subject: Re: new question


Hi.

Thank you your help and sorry only answer now. 

Ok, the boxplots is ok. But I need too by group... on par(mfrow(c(2,2))), I can
have par(mfrow(c(3,2)), for example (or more) and have a boxplot for the group.
You can help me to group them?

About the other function I need to do other things, but now I need to think what
to do...

Thank you





2013/3/18 arun <smartpink111 at yahoo.com>

>
>
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>print(new.list)
>? par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>}
>?z.boxplot(ListFacGroup) #prints new.list
>
>If you want to turn off that:
>
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>#print(new.list)
>? par(mfrow=c(2,2))
>b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>
>
>}
>?z.boxplot(ListFacGroup)
>A.K.
>
>
>
>
>
>________________________________
>From: Vera Costa <veracosta.rt at gmail.com>
>To: arun <smartpink111 at yahoo.com>
>Sent: Monday, March 18, 2013 1:59 PM
>Subject: Re: new question
>
>
>
>For example, if I run you code without "pdf...." and
"dev.off" I have what I want
>
>directory<- "C:/Users/Vera Costa/Desktop/dados.lixo"
>?#modified the function
>GetFileList <- function(directory,number){
>? setwd(directory)
>? filelist1<-dir()
>
>??? lista<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = TRUE, recursive = TRUE)
>????? output<- list(filelist1,lista)
>? return(output)
>???? }
>file.list.names<-GetFileList(directory,23)[[1]]
>lista<-GetFileList(directory,23)[[2]]
>FacGroup<-c(0,1,0,2,2,0,3)
>ReadDir<-function(FacGroup){
>? list.new<-lista[FacGroup!=0]
>? read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
>? names(read.list)<-file.list.names[FacGroup!=0]
>? return (read.list)
>?}
>ListFacGroup<-ReadDir(FacGroup)
>ListFacGroup
>?z.boxplot<- function(lst){
>?new.list<-? lapply(lst,function(x) x[x$FDR<0.01,])
>?print(new.list)
>?#pdf("VeraBP.pdf")
>?par(mfrow=c(2,2))
>?lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
>?#dev.off()
>?}
>?z.boxplot(ListFacGroup)
>
>
>
>
>
>But I have the results too (I don't need it)
>
>
>[[1]]
>[[1]]$a2
>[[1]]$a2$stats
>???????????? [,1]???????? [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[1]]$a2$n
>[1] 8 2
>[[1]]$a2$conf
>????????????? [,1]????????? [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,]? 0.0007270240? 0.0007035253
>[[1]]$a2$out
>[1] 0.00494012
>[[1]]$a2$group
>[1] 1
>[[1]]$a2$names
>[1] "2" "3"
>
>[[2]]
>[[2]]$c2
>[[2]]$c2$stats
>???????????? [,1]???????? [,2]
>[1,] 0.0000000000 0.0000000000
>[2,] 0.0000000000 0.0000000000
>[3,] 0.0001355197 0.0002175095
>[4,] 0.0010588777 0.0004350190
>[5,] 0.0016571381 0.0004350190
>[[2]]$c2$n
>[1] 8 2
>[[2]]$c2$conf
>????????????? [,1]????????? [,2]
>[1,] -0.0004559846 -0.0002685062
>[2,]? 0.0007270240? 0.0007035253
>[[2]]$c2$out
>[1] 0.00494012
>[[2]]$c2$group
>[1] 1
>[[2]]$c2$names
>[1] "2" "3"
>
>[[3]]
>[[3]]$c3
>[[3]]$c3$stats
>??????????? [,1]???????? [,2]
>[1,] 0.000000000 0.0000000000
>[2,] 0.000000000 0.0000000000
>[3,] 0.000000000 0.0000000000
>[4,] 0.002226409 0.0002086594
>[5,] 0.002226409 0.0004173187
>[[3]]$c3$n
>[1] 6 4
>[[3]]$c3$conf
>???????????? [,1]????????? [,2]
>[1,] -0.001436105 -0.0001648409
>[2,]? 0.001436105? 0.0001648409
>[[3]]$c3$out
>[1] 0.00560348
>[[3]]$c3$group
>[1] 1
>[[3]]$c3$names
>[1] "2" "3"
>
>[[4]]
>[[4]]$t2
>[[4]]$t2$stats
>???? [,1]???????? [,2] [,3]
>[1,]??? 0 0.0000000000??? 0
>[2,]??? 0 0.0000000000??? 0
>[3,]??? 0 0.0002908668??? 0
>[4,]??? 0 0.0025929827??? 0
>[5,]??? 0 0.0052577771??? 0
>[[4]]$t2$n
>[1]? 1 10? 5
>[[4]]$t2$conf
>???? [,1]???????? [,2] [,3]
>[1,]??? 0 -0.001004691??? 0
>[2,]??? 0? 0.001586424??? 0
>[[4]]$t2$out
>[1] 0.0092051934 0.0007174888
>[[4]]$t2$group
>[1] 2 3
>[[4]]$t2$names
>[1] "1" "2" "3"
>??????-------------- next part --------------
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arun

2013-Mar-27 04:34 UTC

head link

[R] new question

Hi,
Try this: (Used the old data folder)

Compares the spec counts of sub directory with each other.? 

directory<- "/home/arunksa111/dados"
GetFileList <- function(directory,number){
?setwd(directory)
?filelist1<-dir()[file.info(dir())$isdir]
??? direct<-dir(directory,pattern =
paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
?direct<-lapply(direct,function(x)
paste(directory,"/",x,sep=""))
??? lista<-unlist(direct)
?output<- list(filelist1,lista)
?return(output)
??? }

?
ReadDir<-function(FacGroup){
?list.new<-lista[FacGroup!=0]
?read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep =
"\t"))
?names(read.list)<-file.list.names[FacGroup!=0]
?return (read.list)
}

?file.list.names<-GetFileList(directory,23) [[1]]
?lista<-GetFileList(directory,23) [[2]]

FacGroup<-c(1,1,0,2,2,0,0)
ListFacGroup<-ReadDir(FacGroup)
lst1<-lapply(ListFacGroup,function(x) {x<-within(x,{spec<-
as.character(spec)}); x1<-
x[x$FDR<0.01,c("Seq","Mod","z","spec")];
x1$counts<-sapply(x1$spec,function(x2)
length(unlist(strsplit(x2,","))));x1})
lst2<-lapply(as.data.frame(combn(names(lst1),2),stringsAsFactors=FALSE),function(x)
{
x1<-merge(lst1[[x[1]]],lst1[[x[2]]],by=c("Seq","Mod","z"));names(x1)[c(5,7)]<-
paste0("counts_",c(x[1],x[2]));x1[2,5]<-8;x2<-data.frame(apply(cbind(x1[,5],x1[,7]),1,function(y)
{chisq.test(y)$p.value})); colnames(x2)<-
paste0("Counts_",x[1],x[2]);x2})

####In the above code:, I replaced a count datapoint to make it significant for
the purpose of separating the significant from others ( x1[2,5]<- 8).

?lst3<-lapply(lst2,function(x)
{x1<-list(x[!x[,1]<0.05,],x[x[,1]<0.05,]);names(x1)<-rep(colnames(x),each=2);x1})
?lst3[[5]]
#$Counts_a2c3
#[1] 1 1 1 1 1

#$Counts_a2c3
#[1] 0.01963066


? A.K.




________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Tuesday, March 26, 2013 4:26 PM
Subject: Re: new question (if you could help...)


But you could do the code of t test and chisq.test or not? Thank you
No dia 26 de Mar de 2013 20:16, "arun" <smartpink111 at
yahoo.com> escreveu:

arun

2013-Mar-28 05:05 UTC

head link

[R] new question

Hi,
Regarding the first question:
ListFacGroup<-? lapply(ListFacGroup,unique)
?Spec(ListFacGroup,0.05)
#
?# ????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
#1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 1? 0? 0? 1
#2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 1? 0? 0? 1
#3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
#4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
#5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
#6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
#7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
#8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
#9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
#10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
#11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
#12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
#13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
#14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
#15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
#16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
#17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
#18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
#19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
#20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
#21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
#22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
#23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
#24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0


2nd question: I am not sure I understand it correctly.
A.K.



________________________________
 From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Wednesday, March 27, 2013 7:07 PM
Subject: Re: new question
 

Hi.
With the data in attach,the results has duplicated. I think it's better only
one rows with the information.
The 2nd question,about t test,it's what you did,but for frequencies
directly. You understand? Thank you very much

arun

2013-Mar-28 14:18 UTC

head link

[R] new question

Hi,
Try this:


Spec <- function(lista,FDR_k) {

?list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
?split.list<-split(list.new,names(lista))

?#Data needed with FDR<FDR_k
?seq.mod.z<-lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x)
x[x[["FDR"]]<FDR_k,c("Seq","Mod","z","spec")]))
?names(seq.mod.z)<- names(split.list) 

?#insert colunm with the name of the folder
?folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
?#merge data with the same Seq, Mod and z
?library(plyr)
?library(data.table)
?merge.data<- lapply(folder.name,function(x) lapply(x,function(x1)
{x1<-data.table(x1);
x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))

?#colunm with number of spec
?count.spec<-lapply(merge.data,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
count.specUnique<-lapply(count.spec,function(x) lapply(x,unique))
?#count spec by group (2-columns)
?spec.group<-lapply(count.specUnique,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
? #spec.group1<-spec.group[lapply(spec.group,length)!=0]

?#data frame with count of spec
?res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),spec.group)
?res[is.na(res)] <- 0
res<- as.data.frame(res,stringsAsFactors=FALSE)
?print(res)
}

?Spec(ListFacGroup,0.05)
#?????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
#1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
#2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
#3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
#4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
#5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
#6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
#7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
#8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
#9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
#10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
#11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
#12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
#13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
#14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
#15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
#16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
#17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
#18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
#19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
#20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
#21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
#22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
#23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
#24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0


Regarding the 2nd question, I am a bit busy now.? Will try it later.
A.K.



________________________________
 From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 28, 2013 9:43 AM
Subject: Re: new question
 

I don't remove duplicated, but write only one time. If I haven't
"unique" I have the same row a lot of times, but with
"unique" we remove all. I need this row write only one time.
?
without "unique" the output is 
?
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
2??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
3??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
4??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
5??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
6???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
7???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
8???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
9???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
10??????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
11??????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
12???????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
13????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
14?????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
15??????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
16??????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
17??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
18??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
19????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
20??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
21????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
22??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
23????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
24????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
25???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
26????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
27? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
28? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
29 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
30????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
31???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
32???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
33???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0

?
with "unique" is
?
??????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 1? 0? 0? 1
2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 1? 0? 0? 1
3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0

?
?
But I need the row 
?
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
?
write only one time

arun

2013-Mar-28 18:28 UTC

head link

[R] new question

Hi,
The function outputs the unique rows and also chisq test on frequency ( by row).


Spec <- function(lista,FDR_k) {

?list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
?split.list<-split(list.new,names(lista))

?#Data needed with FDR<FDR_k
?seq.mod.z<-lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x)
x[x[["FDR"]]<FDR_k,c("Seq","Mod","z","spec")]))
?names(seq.mod.z)<- names(split.list) 

?#insert colunm with the name of the folder
?folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
?#merge data with the same Seq, Mod and z
?library(plyr)
?library(data.table)
?merge.data<- lapply(folder.name,function(x) lapply(x,function(x1)
{x1<-data.table(x1);
x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))

?#colunm with number of spec
?count.spec<-lapply(merge.data,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
count.specUnique<-lapply(count.spec,function(x) lapply(x,unique))
?#count spec by group (2-columns)
?spec.group<-lapply(count.specUnique,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
? #spec.group1<-spec.group[lapply(spec.group,length)!=0]

?#data frame with count of spec
?res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),spec.group)
?res[is.na(res)] <- 0
res<- as.data.frame(res,stringsAsFactors=FALSE)
?#print(res)
Chisq1test_Count<-do.call(cbind,lapply(as.data.frame(combn(names(res)[4:ncol(res)],2),stringsAsFactors=FALSE),function(x)
{x1<-data.frame(apply(cbind(res[x[1]],res[x[2]]),1,function(y){ifelse(sum(y)==0,
NA, chisq.test(y)$p.value)}));colnames(x1)<-
paste0("Count_",x[1],x[2]);x1}))
#print(Chisq1test_Count)
res1<- cbind(res,Chisq1test_Count)
res1
}

ListFacGroup<-ReadDir(FacGroup)
Spec(ListFacGroup,0.05)
?head(Spec(ListFacGroup,0.05))
#??????????????????????? Seq???????????????? Mod z a2 c2 c3 t2 Count_a2c2
#1??? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1 0.02534732
#2???? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1 0.01430588
#3????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1 1.00000000
#4?????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1 0.31731051
#5??????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2 1.00000000
#6 aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1 0.31731051
?# Count_a2c3 Count_a2t2 Count_c2c3 Count_c2t2 Count_c3t2
#1 0.02534732 0.10247043???????? NA? 0.3173105? 0.3173105
#2 0.01430588 0.05878172???????? NA? 0.3173105? 0.3173105
#3 0.31731051 1.00000000? 0.3173105? 1.0000000? 0.3173105
#4 1.00000000 1.00000000? 0.3173105? 0.3173105? 1.0000000
#5 0.56370286 1.00000000? 0.5637029? 1.0000000? 0.5637029
#6 0.31731051 1.00000000???????? NA? 0.3173105? 0.3173105

A.K.


________________________________
 From: arun <smartpink111 at yahoo.com>
To: Vera Costa <veracosta.rt at gmail.com> 
Cc: R help <r-help at r-project.org> 
Sent: Thursday, March 28, 2013 10:18 AM
Subject: Re: [R] new question
 
Hi,
Try this:


Spec <- function(lista,FDR_k) {

?list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
?split.list<-split(list.new,names(lista))

?#Data needed with FDR<FDR_k
?seq.mod.z<-lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x)
x[x[["FDR"]]<FDR_k,c("Seq","Mod","z","spec")]))
?names(seq.mod.z)<- names(split.list) 

?#insert colunm with the name of the folder
?folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
?#merge data with the same Seq, Mod and z
?library(plyr)
?library(data.table)
?merge.data<- lapply(folder.name,function(x) lapply(x,function(x1)
{x1<-data.table(x1);
x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))

?#colunm with number of spec
?count.spec<-lapply(merge.data,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
count.specUnique<-lapply(count.spec,function(x) lapply(x,unique))
?#count spec by group (2-columns)
?spec.group<-lapply(count.specUnique,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
? #spec.group1<-spec.group[lapply(spec.group,length)!=0]

?#data frame with count of spec
?res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),spec.group)
?res[is.na(res)] <- 0
res<- as.data.frame(res,stringsAsFactors=FALSE)
?print(res)
}

?Spec(ListFacGroup,0.05)
#?????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
#1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
#2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
#3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
#4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
#5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
#6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
#7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
#8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
#9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
#10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
#11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
#12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
#13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
#14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
#15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
#16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
#17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
#18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
#19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
#20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
#21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
#22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
#23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
#24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0


Regarding the 2nd question, I am a bit busy now.? Will try it later.
A.K.



________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 28, 2013 9:43 AM
Subject: Re: new question


I don't remove duplicated, but write only one time. If I haven't
"unique" I have the same row a lot of times, but with
"unique" we remove all. I need this row write only one time.
?
without "unique" the output is 
?
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
2??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
3??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
4??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
5??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
6???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
7???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
8???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
9???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
10??????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
11??????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
12???????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
13????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
14?????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
15??????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
16??????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
17??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
18??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
19????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
20??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
21????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
22??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
23????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
24????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
25???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
26????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
27? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
28? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
29 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
30????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
31???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
32???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
33???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0

?
with "unique" is
?
??????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 1? 0? 0? 1
2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 1? 0? 0? 1
3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0

?
?
But I need the row 
?
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
?
write only one time

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

arun

2013-Mar-28 18:47 UTC

head link

[R] new question

Hi,
You also mentioned about separating the significant from the non-significant.

If you replace:
Chisq1test_Count<-do.call(cbind,lapply(as.data.frame(combn(names(res)[4:ncol(res)],2),stringsAsFactors=FALSE),function(x)
{x1<-data.frame(apply(cbind(res[x[1]],res[x[2]]),1,function(y){ifelse(sum(y)==0,
NA, chisq.test(y)$p.value)}));colnames(x1)<-
paste0("Count_",x[1],x[2]);x1}))
res1<- cbind(res,Chisq1test_Count)

with
Chisqtest_CountNew<-do.call(cbind,lapply(as.data.frame(combn(names(res)[4:ncol(res)],2),stringsAsFactors=FALSE),function(x)
{x1<-data.frame(apply(cbind(res[x[1]],res[x[2]]),1,function(y){ifelse(sum(y)==0,
NA, chisq.test(y)$p.value)}));colnames(x1)<-
paste0("Count_",x[1],x[2]);x2<-within(x1,{Flag<-ifelse(x1[,1]<0.05,"S","NS")});
colnames(x2)[2]<-paste0(colnames(x2)[1],"_Flag");x2}))
res1<- cbind(res,Chisqtest_CountNew)

in the Spec(),
head(Spec(ListFacGroup,0.05),2)
#???????????????????? Seq??????? Mod z a2 c2 c3 t2 V1.Count_a2c2
#1 aAAAAAAAAAAAAAATATAGPR 1-n_acPro/ 2? 5? 0? 0? 1??? 0.02534732
#2? aAAAAAAAAAAASSPVGVGQR 1-n_acPro/ 2? 6? 0? 0? 1??? 0.01430588
#? V1.Count_a2c2_Flag V2.Count_a2c3 V2.Count_a2c3_Flag V3.Count_a2t2
#1????????????????? S??? 0.02534732????????????????? S??? 0.10247043
#2????????????????? S??? 0.01430588????????????????? S??? 0.05878172
#? V3.Count_a2t2_Flag V4.Count_c2c3 V4.Count_c2c3_Flag V5.Count_c2t2
#1???????????????? NS??????????? NA?????????????? <NA>???? 0.3173105
#2???????????????? NS??????????? NA?????????????? <NA>???? 0.3173105
?# V5.Count_c2t2_Flag V6.Count_c3t2 V6.Count_c3t2_Flag
#1???????????????? NS???? 0.3173105???????????????? NS
#2???????????????? NS???? 0.3173105???????????????? NS


A.K.





----- Original Message -----
From: arun <smartpink111 at yahoo.com>
To: Vera Costa <veracosta.rt at gmail.com>
Cc: R help <r-help at r-project.org>
Sent: Thursday, March 28, 2013 2:28 PM
Subject: Re: [R] new question

Hi,
The function outputs the unique rows and also chisq test on frequency ( by row).


Spec <- function(lista,FDR_k) {

?list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
?split.list<-split(list.new,names(lista))

?#Data needed with FDR<FDR_k
?seq.mod.z<-lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x)
x[x[["FDR"]]<FDR_k,c("Seq","Mod","z","spec")]))
?names(seq.mod.z)<- names(split.list) 

?#insert colunm with the name of the folder
?folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
?#merge data with the same Seq, Mod and z
?library(plyr)
?library(data.table)
?merge.data<- lapply(folder.name,function(x) lapply(x,function(x1)
{x1<-data.table(x1);
x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))

?#colunm with number of spec
?count.spec<-lapply(merge.data,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
count.specUnique<-lapply(count.spec,function(x) lapply(x,unique))
?#count spec by group (2-columns)
?spec.group<-lapply(count.specUnique,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
? #spec.group1<-spec.group[lapply(spec.group,length)!=0]

?#data frame with count of spec
?res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),spec.group)
?res[is.na(res)] <- 0
res<- as.data.frame(res,stringsAsFactors=FALSE)
?#print(res)
Chisq1test_Count<-do.call(cbind,lapply(as.data.frame(combn(names(res)[4:ncol(res)],2),stringsAsFactors=FALSE),function(x)
{x1<-data.frame(apply(cbind(res[x[1]],res[x[2]]),1,function(y){ifelse(sum(y)==0,
NA, chisq.test(y)$p.value)}));colnames(x1)<-
paste0("Count_",x[1],x[2]);x1}))
#print(Chisq1test_Count)
res1<- cbind(res,Chisq1test_Count)
res1
}

ListFacGroup<-ReadDir(FacGroup)
Spec(ListFacGroup,0.05)
?head(Spec(ListFacGroup,0.05))
#??????????????????????? Seq???????????????? Mod z a2 c2 c3 t2 Count_a2c2
#1??? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1 0.02534732
#2???? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1 0.01430588
#3????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1 1.00000000
#4?????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1 0.31731051
#5??????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2 1.00000000
#6 aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1 0.31731051
?# Count_a2c3 Count_a2t2 Count_c2c3 Count_c2t2 Count_c3t2
#1 0.02534732 0.10247043???????? NA? 0.3173105? 0.3173105
#2 0.01430588 0.05878172???????? NA? 0.3173105? 0.3173105
#3 0.31731051 1.00000000? 0.3173105? 1.0000000? 0.3173105
#4 1.00000000 1.00000000? 0.3173105? 0.3173105? 1.0000000
#5 0.56370286 1.00000000? 0.5637029? 1.0000000? 0.5637029
#6 0.31731051 1.00000000???????? NA? 0.3173105? 0.3173105

A.K.


________________________________
From: arun <smartpink111 at yahoo.com>
To: Vera Costa <veracosta.rt at gmail.com> 
Cc: R help <r-help at r-project.org> 
Sent: Thursday, March 28, 2013 10:18 AM
Subject: Re: [R] new question

Hi,
Try this:


Spec <- function(lista,FDR_k) {

?list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
?split.list<-split(list.new,names(lista))

?#Data needed with FDR<FDR_k
?seq.mod.z<-lapply(seq_along(split.list),function(i)
lapply(split.list[[i]],function(x)
x[x[["FDR"]]<FDR_k,c("Seq","Mod","z","spec")]))
?names(seq.mod.z)<- names(split.list) 

?#insert colunm with the name of the folder
?folder.name<-lapply(seq.mod.z,function(x) lapply(names(x),function(i)
do.call(rbind,lapply(x[i],function(x) cbind(folder_name=i,x)))))
?#merge data with the same Seq, Mod and z
?library(plyr)
?library(data.table)
?merge.data<- lapply(folder.name,function(x) lapply(x,function(x1)
{x1<-data.table(x1);
x1[,spec:=paste(spec,collapse=","),by=c("Seq","Mod","z")]}))

?#colunm with number of spec
?count.spec<-lapply(merge.data,function(x) lapply(x,function(x1)
{x1$counts<-sapply(x1$spec, function(x2) length(gsub("\\s",
"", unlist(strsplit(x2,
",")))));x3<-as.data.frame(x1);names(x3)[6]<-
as.character(unique(x3$folder_name));x3[,-c(1,5)]}))
count.specUnique<-lapply(count.spec,function(x) lapply(x,unique))
?#count spec by group (2-columns)
?spec.group<-lapply(count.specUnique,function(x) Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),x))
? #spec.group1<-spec.group[lapply(spec.group,length)!=0]

?#data frame with count of spec
?res<- Reduce(function(...)
merge(...,by=c("Seq","Mod","z"),all=TRUE),spec.group)
?res[is.na(res)] <- 0
res<- as.data.frame(res,stringsAsFactors=FALSE)
?print(res)
}

?Spec(ListFacGroup,0.05)
#?????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
#1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
#2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
#3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
#4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
#5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
#6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
#7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
#8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
#9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
#10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
#11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
#12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
#13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
#14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
#15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
#16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
#17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
#18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
#19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
#20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
#21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
#22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
#23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
#24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0


Regarding the 2nd question, I am a bit busy now.? Will try it later.
A.K.



________________________________
From: Vera Costa <veracosta.rt at gmail.com>
To: arun <smartpink111 at yahoo.com> 
Sent: Thursday, March 28, 2013 9:43 AM
Subject: Re: new question


I don't remove duplicated, but write only one time. If I haven't
"unique" I have the same row a lot of times, but with
"unique" we remove all. I need this row write only one time.
?
without "unique" the output is 
?
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
2??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
3??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
4??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
5??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
6???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
7???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
8???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
9???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
10??????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
11??????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 6? 0? 0? 1
12???????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
13????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
14?????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
15??????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
16??????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
17??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
18??????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
19????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
20??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
21????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
22??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
23????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
24????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
25???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
26????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
27? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
28? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
29 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
30????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
31???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
32???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
33???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0

?
with "unique" is
?
??????????????????????????????? Seq???????????????? Mod z a2 c2 c3 t2
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 1? 0? 0? 1
2???????????? aAAAAAAAAAAASSPVGVGQR????????? 1-n_acPro/ 2? 1? 0? 0? 1
3????????????????? aAAAAAAAAAGAAGGR????????? 1-n_acPro/ 2? 1? 1? 0? 1
4?????????????????????? AAAAAAALQAK???????????????????? 2? 1? 0? 1? 1
5??????????????????? aAAAAAGAGPEMVR????????? 1-n_acPro/ 2? 2? 2? 1? 2
6???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 2? 1? 0? 0? 1
7???????? aAAAAEQQQFYLLLGNLLSPDNVVR 1-<_Carbamoylation/ 3? 1? 0? 0? 1
8???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 2? 0? 1? 0? 0
9???????? aAAAAEQQQFYLLLGNLLSPDNVVR????????? 1-n_acPro/ 3? 1? 2? 2? 1
10????????????????????? AAAAAPGTAEK???????????????????? 2? 0? 1? 0? 0
11??????????? aAAAASAPQQLSDEELFSQLR????????? 1-n_acPro/ 2? 1? 0? 0? 1
12????????????????? aAAAAVGNAVPCGAR????????? 1-n_acPro/ 2? 1? 1? 1? 1
13??????????????? AAAAAWEEPSSGNGTAR???????????????????? 2? 1? 1? 1? 1
14????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 1? 1? 0? 0? 1
15????????????????????? aAAAELSLLEK????????? 1-n_acPro/ 2? 1? 1? 1? 1
16???????????????????? AAAAEVLGLILR???????????????????? 2? 1? 1? 1? 1
17????? aAAAGAAAAAAAEGEAPAEMGALLLEK????????? 1-n_acPro/ 3? 1? 1? 1? 1
18? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR 1-<_Carbamoylation/ 3? 0? 0? 1? 0
19? aAAAGGGGPGTAVGATGSGIAAAAAGLAVYR????????? 1-n_acPro/ 3? 1? 0? 0? 1
20 aAAANSGSSLPLFDCPTWAGKPPPGLHLDVVK????????? 1-n_acPro/ 3? 1? 0? 0? 1
21????????????????????? AAAAAAAkAAK???????????? 8-K_ac/ 2? 0? 1? 0? 0
22???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 2? 0? 1? 1? 0
23???????? aAAAVGAGHGAGGPGAASSSGGAR????????? 1-n_acPro/ 3? 0? 0? 1? 0
24???????????? aAADGDDSLYPIAVLIDELR????????? 1-n_acPro/ 2? 0? 0? 1? 0

?
?
But I need the row 
?
1??????????? aAAAAAAAAAAAAAATATAGPR????????? 1-n_acPro/ 2? 5? 0? 0? 1
?
write only one time

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______________________________________________
R-help at r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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