SGOL plot
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viritha kaza ▴ 580
@viritha-kaza-4318
Last seen 7.1 years ago
Hi John, I had asked you of some questions regarding cghMCR. Before my data use to give a SGOL plot. I am not sure if there is any little change that I am doing. Code: >source("http://bioconductor.org/biocLite.R") >biocLite(c("CNTools","cghMCR")) > library(CNTools) >require(CNTools, quietly = TRUE) >data2<-read.table("Goutput_chr_1.txt",sep='\t',header=TRUE,colClasses =c('character','character','numeric','numeric','numeric', 'numeric')) >head(data2) ID chrom loc.start loc.end num.mark seg.mean 1 G20020876 1 604268 797005 6 0.0000000 2 G20020876 1 807922 1145639 46 0.5746844 3 G20020876 1 1149781 3558855 256 0.9192132 4 G20020876 1 3563712 3563759 1 -1.1201798 5 G20020876 1 3568451 3981215 44 0.9192132 6 G20020876 1 3988891 4769811 60 0.5746844 > data(geneInfo) >set.seed(1234) > convertedData<-getRS(CNSeg(data2[which(is.element(data2[,"ID"],sampl e(unique(data2[,"ID"]),10))),]),by = "gene", imput=FALSE,XY=FALSE,geneMap=geneInfo) Error in match.arg(what) : 'arg' must be of length 1 I am not able to understand what is this error and how to execute to finally get sgol plot. If you could figure out what is the issue that would be grateful. waiting for your reply, Thanks, [[alternative HTML version deleted]]
cghMCR cghMCR • 738 views
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@pascalgellert-8260
Last seen 6.3 years ago
United Kingdom

Hi,

I think you have to add what="mean" or what="median" as argument to the getRS function. This argument was explained in a previous version of CNTools and apparently it does not run without it

convertedData<-getRS(CNSeg(data2[which(is.element(data2[,"ID"],sampl e(unique(data2[,"ID"]),10))),]),by = "gene", imput=FALSE,XY=FALSE,geneMap=geneInfo, what="mean")

Pascal