file（file，“ rt”）R参数错误

Question

i am using below RScript.

/usr/local/bin/R CMD BATCH --slave '--args 51102' coverage_db/src/main/scripts/R_ExonsPlots.R

R Script as follows

args<-commandArgs(TRUE)
gname = as.numeric(args[1])
sample_data = read.table(Sys.glob("/NGS_STORE/ARCHIVE2/Cov_InputBed_Repository/*gname*"),sep="\t",header=FALSE,stringsAsFactors=FALSE)
colnames(sample_data)=c("chr","start","end","gene","avg_depth")

Error

Error in file(file, "rt") : invalid 'description' argument 

It worked fine without "arguments" but could not get what the error is

Answer 1

The error results from read.table because multiple filenames are returned by the Sys.glob . In this case, Sys.glob will return a vector of characters, one for each file name matching the wildcard. Most likely, this problem is triggered by the other problem where the value for gname is actually not used since "/NGS_STORE/ARCHIVE2/Cov_InputBed_Repository/*gname*" is just a string (characters). To fix both:

args<-commandArgs(TRUE)
gname = as.numeric(args[1])
files = Sys.glob(paste0("/NGS_STORE/ARCHIVE2/Cov_InputBed_Repository/*",gname,"*"))
if (!is.na(files[1])) {
  sample_data = data.frame()
  for (afile in files) {
      sample_data = rbind(sample_data, read.table(afile, sep="\t", header=FALSE,
                                                  stringsAsFactors=FALSE))
  }
  colnames(sample_data)=c("chr","start","end","gene","avg_depth")
}

Here, I'm assuming that if there are multiple files satisfying the glob, you want to combine them by rows (ie, they have the same number of columns). Obviously, you can combine them by columns, ignore all but the first, etc.

Note that if there are no matches for the glob, then it will return NA . That is why we need to check for NA before calling read.table . Otherwise, you will get the read.table error Error in file(file, "rt") : cannot open the connection .