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Sariya, Sanjeev

2018-Mar-05 19:06 UTC

[R] Help with apply and new column?

Thanks. I think nabble is good for programming questions. Bear with me if
I'm incorrect.

Data: Genomics SNP information 
Goal: I need to add Chromosome and SNP position to the data frame I'm using
through apply.

I'd like to add new column from text processed through apply function.

For example:  10:60523:T:G  (Column 2)
CHR: 10
Position: 60523

Dataset:
chr	rs	ps	n_miss	allele1	allele0	af	beta	se	l_remle	p_wald
-9	10:60523:T:G	-9	0	T	G	0.977	-1.769354e-02	3.597196e-02	1.566731e-01
6.228309e-01
-9	10:60684:A:C	-9	0	A	C	0.973	1.698925e-02	2.942366e-02	1.561001e-01
5.636926e-01
-9	10:61331:A:G	-9	0	A	G	0.973	1.708586e-02	2.942424e-02	1.560944e-01
5.614851e-01
-9	10:62010:C:T	-9	0	C	T	0.980	-8.513143e-03	3.837054e-02	1.566875e-01
8.244260e-01

Code:

--------------------------------------------------------
data<-read.table("small.txt",header = T) # read data
data<-data[,c(2,11)] #delete other columns not needed 

#--split data on : and get chromosome and position

split_rs<-function(rs){  
    
    chr<-vector(,length(rs)) # create new vector to store chr
    pos<-vector(,length(rs)) #create new vector to store position
    
    for(i in 1:length(rs)){ #iterate over RS column

        if(grepl(":",rs[i])){ #if : in column string 
            temp <- strsplit(rs[i],":",fixed=T)         #split
            chr[i] <-temp[[1]][1] #store CHR
            pos[i] <- temp[[1]][2]  #store position
        }    
    }
    return(list(chr=chr,pos=pos)) #return making a list
}

data$POS<-"NA" #add new column CHR and make NA 
data$CHR <- "NA" #add new column POS and make NA

temp<-apply(data,2,split_rs) #send data frame to function 

#--I assign value from list sent -- I would like to improve this part

data$CHR<-temp$rs$chr
data$POS<-temp$rs$pos

rm(temp)

colnames(data)<-c("SNP","P","CHR","BP")
--------------------------------------------------------



-----Original Message-----
From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] 
Sent: Monday, March 5, 2018 1:48 PM
To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at
cumc.columbia.edu>; R Help <r-help at r-project.org>
Subject: Re: [R] Help with apply and new column?

Read the Posting Guide... (see message footer) ... some relevant things you can
find there:

a) Yes, this appears to be about how to use an R base function so it is on topic
b) Post a reproducible example (include some sample data, preferably using the
dput function)
c) Post using plain text so the mailing list doesn't convert it for you and
mangle things in a way you did not intend.
--
Sent from my phone. Please excuse my brevity.

On March 5, 2018 10:07:24 AM PST, "Sariya, Sanjeev" <ss5505 at
cumc.columbia.edu> wrote:>Hello members,
>
>Can I ask question for apply, adding new column to data frame on this 
>e-mail list?
>
>Thanks!
>
>
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
>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.

Jeff Newmiller

2018-Mar-05 20:36 UTC

head link

[R] Help with apply and new column?

Comments interspersed, and some code at the end.

On Mon, 5 Mar 2018, Sariya, Sanjeev wrote:
> Thanks. I think nabble is good for programming questions. Bear with me 
> if I'm incorrect.
You may have found R-help archives at Nabble, but R-help has nothing to do 
with Nabble.
>
> Data: Genomics SNP information
I know almost nothing about using R for genomics.
> Goal: I need to add Chromosome and SNP position to the data frame I'm
using through apply.
>
> I'd like to add new column from text processed through apply function.
>
> For example:  10:60523:T:G  (Column 2)
> CHR: 10
> Position: 60523
Assuming Position is "P", what are your "SNP" and
"BP" in the names you
assigned below as
c("SNP","P","CHR","BP")?
> Dataset:
> chr	rs	ps	n_miss	allele1	allele0	af	beta	se	l_remle	p_wald
> -9	10:60523:T:G	-9	0	T	G	0.977	-1.769354e-02	3.597196e-02	1.566731e-01
6.228309e-01
> -9	10:60684:A:C	-9	0	A	C	0.973	1.698925e-02	2.942366e-02	1.561001e-01
5.636926e-01
> -9	10:61331:A:G	-9	0	A	G	0.973	1.708586e-02	2.942424e-02	1.560944e-01
5.614851e-01
> -9	10:62010:C:T	-9	0	C	T	0.980	-8.513143e-03	3.837054e-02	1.566875e-01
8.244260e-01
>
> Code:
>
> --------------------------------------------------------
> data<-read.table("small.txt",header = T) # read data
> data<-data[,c(2,11)] #delete other columns not needed
>
> #--split data on : and get chromosome and position
>
> split_rs<-function(rs){
>
>    chr<-vector(,length(rs)) # create new vector to store chr
>    pos<-vector(,length(rs)) #create new vector to store position
>
>    for(i in 1:length(rs)){ #iterate over RS column
>
>        if(grepl(":",rs[i])){ #if : in column string
>            temp <- strsplit(rs[i],":",fixed=T)         #split
>            chr[i] <-temp[[1]][1] #store CHR
>            pos[i] <- temp[[1]][2]  #store position
>        }
>    }
>    return(list(chr=chr,pos=pos)) #return making a list
> }
>
> data$POS<-"NA" #add new column CHR and make NA
> data$CHR <- "NA" #add new column POS and make NA
>
> temp<-apply(data,2,split_rs) #send data frame to function
>
> #--I assign value from list sent -- I would like to improve this part
>
> data$CHR<-temp$rs$chr
> data$POS<-temp$rs$pos
>
> rm(temp)
>
>
colnames(data)<-c("SNP","P","CHR","BP")
> --------------------------------------------------------
######################################################
# Your code was pretty severely broken... it would not run,
# and I don't know what you expected to see as output.

# 1) data is the name of a function in base R... re-using
#    it can lead to puzzling errors
# 2) With all this character manipulation, you need to read
#    your character data in as character, not as factors
# 3) Don't use the T variable... use the constant TRUE,
#    since T can easily be overwritten to some non-TRUE value.
dta <- read.table( "small.txt", header = TRUE, as.is = TRUE ) #
read data
dta <- dta[ , c( 2, 11 ) ] #delete other columns not needed

# 4) Not at all clear why you want to split all of the columns
#    using apply( ..., 2, ... ) when only one column has ":"
characters
#temp <- apply( dta, 2, split_rs ) #send data frame to function
temp <- strsplit( dta$rs, ":" ) # gets the whole column splits at
once

# wildly guessing here
rs_chrmatrix <- do.call( rbind, temp )
rs_DF <- as.data.frame( rs_chrmatrix, stringsAsFactors = FALSE )
names( rs_DF ) <- c( "CHR", "P", "X1",
"X2" )
rs_DF$P <- as.integer( rs_DF$P )

str( rs_DF )
##################################################



>
> -----Original Message-----
> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
> Sent: Monday, March 5, 2018 1:48 PM
> To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at
cumc.columbia.edu>; R Help <r-help at r-project.org>
> Subject: Re: [R] Help with apply and new column?
>
> Read the Posting Guide... (see message footer) ... some relevant things you
can find there:
>
> a) Yes, this appears to be about how to use an R base function so it is on
topic
> b) Post a reproducible example (include some sample data, preferably using
the dput function)
> c) Post using plain text so the mailing list doesn't convert it for you
and mangle things in a way you did not intend.
> --
> Sent from my phone. Please excuse my brevity.
>
> On March 5, 2018 10:07:24 AM PST, "Sariya, Sanjeev" <ss5505 at
cumc.columbia.edu> wrote:
>> Hello members,
>>
>> Can I ask question for apply, adding new column to data frame on this
>> e-mail list?
>>
>> Thanks!
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
Go...
                                       Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k

Sariya, Sanjeev

2018-Mar-05 21:12 UTC

head link

[R] Help with apply and new column?

Thank you, that helps. 

-----Original Message-----
From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] 
Sent: Monday, March 5, 2018 3:36 PM
To: Sariya, Sanjeev <ss5505 at cumc.columbia.edu>
Cc: r-help at r-project.org; R Help <r-help at r-project.org>
Subject: RE: [R] Help with apply and new column?

Comments interspersed, and some code at the end.

On Mon, 5 Mar 2018, Sariya, Sanjeev wrote:
> Thanks. I think nabble is good for programming questions. Bear with me 
> if I'm incorrect.
You may have found R-help archives at Nabble, but R-help has nothing to do with
Nabble.
>
> Data: Genomics SNP information
I know almost nothing about using R for genomics.
> Goal: I need to add Chromosome and SNP position to the data frame I'm
using through apply.
>
> I'd like to add new column from text processed through apply function.
>
> For example:  10:60523:T:G  (Column 2)
> CHR: 10
> Position: 60523
Assuming Position is "P", what are your "SNP" and
"BP" in the names you assigned below as
c("SNP","P","CHR","BP")?
> Dataset:
> chr	rs	ps	n_miss	allele1	allele0	af	beta	se	l_remle	p_wald
> -9	10:60523:T:G	-9	0	T	G	0.977	-1.769354e-02	3.597196e-02	1.566731e-01
6.228309e-01
> -9	10:60684:A:C	-9	0	A	C	0.973	1.698925e-02	2.942366e-02	1.561001e-01
5.636926e-01
> -9	10:61331:A:G	-9	0	A	G	0.973	1.708586e-02	2.942424e-02	1.560944e-01
5.614851e-01
> -9	10:62010:C:T	-9	0	C	T	0.980	-8.513143e-03	3.837054e-02	1.566875e-01
8.244260e-01
>
> Code:
>
> --------------------------------------------------------
> data<-read.table("small.txt",header = T) # read data 
> data<-data[,c(2,11)] #delete other columns not needed
>
> #--split data on : and get chromosome and position
>
> split_rs<-function(rs){
>
>    chr<-vector(,length(rs)) # create new vector to store chr
>    pos<-vector(,length(rs)) #create new vector to store position
>
>    for(i in 1:length(rs)){ #iterate over RS column
>
>        if(grepl(":",rs[i])){ #if : in column string
>            temp <- strsplit(rs[i],":",fixed=T)         #split
>            chr[i] <-temp[[1]][1] #store CHR
>            pos[i] <- temp[[1]][2]  #store position
>        }
>    }
>    return(list(chr=chr,pos=pos)) #return making a list }
>
> data$POS<-"NA" #add new column CHR and make NA data$CHR <-
"NA" #add
> new column POS and make NA
>
> temp<-apply(data,2,split_rs) #send data frame to function
>
> #--I assign value from list sent -- I would like to improve this part
>
> data$CHR<-temp$rs$chr
> data$POS<-temp$rs$pos
>
> rm(temp)
>
>
colnames(data)<-c("SNP","P","CHR","BP")
> --------------------------------------------------------
######################################################
# Your code was pretty severely broken... it would not run, # and I don't
know what you expected to see as output.

# 1) data is the name of a function in base R... re-using
#    it can lead to puzzling errors
# 2) With all this character manipulation, you need to read
#    your character data in as character, not as factors
# 3) Don't use the T variable... use the constant TRUE,
#    since T can easily be overwritten to some non-TRUE value.
dta <- read.table( "small.txt", header = TRUE, as.is = TRUE ) #
read data dta <- dta[ , c( 2, 11 ) ] #delete other columns not needed

# 4) Not at all clear why you want to split all of the columns
#    using apply( ..., 2, ... ) when only one column has ":"
characters
#temp <- apply( dta, 2, split_rs ) #send data frame to function temp <-
strsplit( dta$rs, ":" ) # gets the whole column splits at once

# wildly guessing here
rs_chrmatrix <- do.call( rbind, temp )
rs_DF <- as.data.frame( rs_chrmatrix, stringsAsFactors = FALSE ) names( rs_DF
) <- c( "CHR", "P", "X1", "X2" )
rs_DF$P <- as.integer( rs_DF$P )

str( rs_DF )
##################################################



>
> -----Original Message-----
> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us]
> Sent: Monday, March 5, 2018 1:48 PM
> To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at
cumc.columbia.edu>;
> R Help <r-help at r-project.org>
> Subject: Re: [R] Help with apply and new column?
>
> Read the Posting Guide... (see message footer) ... some relevant things you
can find there:
>
> a) Yes, this appears to be about how to use an R base function so it 
> is on topic
> b) Post a reproducible example (include some sample data, preferably 
> using the dput function)
> c) Post using plain text so the mailing list doesn't convert it for you
and mangle things in a way you did not intend.
> --
> Sent from my phone. Please excuse my brevity.
>
> On March 5, 2018 10:07:24 AM PST, "Sariya, Sanjeev" <ss5505 at
cumc.columbia.edu> wrote:
>> Hello members,
>>
>> Can I ask question for apply, adding new column to data frame on this 
>> e-mail list?
>>
>> Thanks!
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 
>> 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.
>
---------------------------------------------------------------------------
Jeff Newmiller                        The     .....       .....  Go Live...
DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
Go...
                                       Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
/Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k

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