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.
