[R] undefined columns selected

Bert Gunter bgunter@4567 @end|ng |rom gm@||@com
Wed Dec 4 01:08:54 CET 2019


Basically no clue, but note that C[, 1:length(C[ ,1])] looks suspect -- you
are selecting the number of columns equal to the number of rows in C. Is
that really what you want to do?

Bert

On Tue, Dec 3, 2019, 2:36 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:

> Hello,
>
> I am trying to run this software:
>
> https://github.com/eleporcu/TWMR
>
> and I have my input files in my current directory: ENSG00000154803.matrix,
> ENSG00000154803.ld
>
> but when I try to run it:
>
> Rscript MR.R ENSG00000154803
>
> [1] "ENSG00000154803"
> Error in `[.data.frame`(C, , 1:length(C[, 1])) :
>   undefined columns selected
> Calls: as.matrix -> [ -> [.data.frame
> Execution halted
>
> I should mention that I was able to run this script before with the same
> command when I had input like:
> https://github.com/eleporcu/TWMR/blob/master/ENSG00000000971.matrix
>
> and I also, per suggestion changed the beginning of the code to be:
> cmd_args <- commandArgs(TRUE)
> if (length(cmd_args) == 0L) stop("No arguments specified.")
> print(cmd_args)
> gene<-cmd_args[length(cmd_args)]   ## Last argument is the 'gene'
> Ngwas<-239087
> N_eQTLs<-32000
> out<-c("gene","alpha","SE","P","Nsnps","Ngene")
>
> file<-paste(gene,"matrix",sep=".")
> if (!file.exists(file)) stop("File not found: ", file)
> filecluster<-read.table(file,header=T,sep=" ",dec=".")
> beta<-as.matrix(filecluster[,2:(length(filecluster[1,])-1)])
>
> now my input is like this:
>
> https://github.com/eleporcu/TWMR/blob/master/ENSG00000000419.matrix
>
> so 4 columns instead of 3 like it was before and when I run it I get that
> error above.
>
> Please advise,
> Ana
>
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>
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