Hi all,
This is perhaps very basic to the R pros, but I was wondering how I could assign a variable, say "control" to a string of sorts. For example:
"musclenormal15494"
"musclenormal15497"
"musclenormal15501"
My interest is in the muscle_normal part and since it's quite a list, it will be quite hectic to assign each one individually.
Any suggestions will be greatly appreciated.
Thanks.
-Avoks
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written
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Avoks •
1 answer
I guess what you want is:
x=c("muscle_normal_15494","muscle_normal_15497","muscle_normal_15501","the_other_string_1","the_other_string_2")
myfactors=rep(NA,length(x))
myfactors[grep("muscle_normal",x)]="control"
myfactors[grep("the_other_string",x)]="other"
myfactors=as.factor(myfactors)
This is just an example, you absolutely should not need to enter these by hand! If this is stored in a file, you can of course read the file with x=read.table("myfile"), if it is a list, you just have to unlist() it first. How is your data stored?
Actually now I read through again, I kind of get it. I however got the info I wanted by sorting and extracting by numbers:
groups = pData(phenoData(gsexxxxxdat[[1]]))$title
groups=as.character(groups)
groups=sort(groups)
groups[c(1:45)]="T2D"
groups[c(46:71)]="IGT"
groups[c(72:118)]="control"
f = factor(groups, levels=c("control","T2D","IGT"))
Perhaps not the most intuitive way but I got what I wanted:).
Thanks again.
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Hi, Sorry its unclear to me, do you have list with strings given above stored in it, and you want to filter the ones starting with muscle_normal and store it in other list!!
Hi Sukhdeep. These are gse18732 data I extracted from GEO using getGEO. I'm running a limma analysis and trying to assign the different cases to the 3 test levels, T2D, IGT and Control(normal) so that I can create an appropriate cont. matrix. I usually use a different "channel" but for this particular study the channels are quite confusing and the "title" seemed to be the most straightforward but it comes with the numbers, hence my question.