Displaying 7 results from an estimated 7 matches for "geneb".
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genet
2011 Mar 23
1
how to add in interaction terms in gamm
I want to use gamm to generate smoothed trend line for three groups
identified by dummy variable genea and geneb. My question is how to add in
an interaction term between the time and another dummy variable such as
gender?
fitm<-gamm(change_gfr~
genea+geneb+s(timea_n,bs="ps")+s(timeb_n,bs="ps")+s(timec_n,bs="ps"),data=mm,random=list(time_n=~1|PID))
--
View this message in c...
2008 Feb 06
1
Histogram/Bar plot graph
Hi,
I have the following data:
> Myvalues
Gene ES MEF Embryo ESHyp
1 GeneA -0.38509507 0.00 1.6250 1.7039921
2 GeneB 0.06262914 0.00 1.6250 -0.272033
and so on...
I want to plot the expression values of GeneA and GeneB in the
different cell/embryo/conditions (columns 2:5 above). Now, if I do:
>library(ggplot2)
> qplot(x=Gene, Embryo, geom = "bar")
I get a plot of GeneA, B...so on only for t...
2018 May 25
2
how to make the code more efficient using lapply
...store the extracted result from each
excel file inside for-loop
for (i in list.files()) { # loop through each excel file in the directory
temp<-read_xlsx(i,sheet=1,range=cell_cols(c(1,30,38:42))) # from package
"readxl" to read in excel file
temp<-temp[grep("^geneA$|^geneB$|^geneC$",temp$Id),] # extract rows
based on temp$id
names(temp)<-gsub("^.*] ","",names(temp)) # clean up column names
temp.df<-append(temp.df, list(as.data.frame(temp))) # change the
dataframe to list, so it can be append to list.
if (i == list.files()[len...
2018 May 25
0
how to make the code more efficient using lapply
...s. As it is you are calling
list.files() each time
through the loop which could be slow.
In any case here's a possible way to do it. Warning: untested!
f <- function(fn) {
temp<-read_xlsx(fn,sheet=1,range=cell_cols(c(1,30,38:42)))
temp<-temp[temp$Id %in% c("geneA","geneB","geneC"),]
}
myL <- lapply( X=list.files(), FUN=f )
temp.df.all<-do.call("rbind",myL)
names(temp.df.all)<-gsub("^.*] ","",names(temp.df.all))
write_xlsx(temp.df.all, path="output.xlsx")
HTH,
Eric
On Fri, May 25, 2018 at 9:24 AM,...
2018 May 25
1
how to make the code more efficient using lapply
...vector, and use the vector inside the loop.
Here's another way (also untested).
infiles <- list.files()
nfiles <- length(infiles)
## read the first file
dfall <- read_xlsx(infiles[1], sheet=1, range=cell_cols(c(1,30,38:42)))
dfall <- dfall[dfall$Id %in% c("geneA","geneB","geneC") , ]
## I'm going to assume the colnames are all the same on input
## if that's wrong, then they have to be fixed inside the loop
## read the remaining files, appending their contents each time
for (ifl in 2:nfiles) {
temp <- read_xlsx(infiles[ifl], sheet=1, r...
2011 Sep 21
1
Problem indexing a factor variable
...mples and 27000 columns of gene expression measurements with each column corresponding to one gene. I now have a smaller vector of genes "tp" for which I need to pull out the data form the data frame.
# first gene from the list with 16 genes
x <- tp[1,]
x
[1] geneA
16 Levels: geneA, geneB...
#unsuccessful
gexp_1$x
NULL
#or
gexp_1$x[1]
NULL
#but this works
gexp_1$geneA
I am sure that this is a fundamental error on my part since I am new to R, I would appreciate any advice. I am trying to construct a for loop to analyze data for sets of genes at a time but stuck at this step.
Re...
2004 Feb 15
8
Wifi Phones
Hello list, I was going to buy this weekend a Wisip from
http://www.pulverinnovations.com/, but jeff got out of stock and he wont
have Wisip for the next 3 to 4 weeks. So I start searching for other
wifi phones because I was really upset about it and I found IPC5000 from
http://www.fahdtel.com/sip_phones.htm, I liked so much the pic that I
email the guy and he send me the PDF with all the details