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.anamar...@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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@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. > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
