Reading files in R inside a bash loop - r

Question

I want to run a R script for 23 chromosomes. The files I need to read are "chr_1.txt, chr_2.txt,...,chr_23.txt"
So I have a bash file
#!/bin/bash
for chr in {1..23}; do \
sbatch torunR.sh "chr_$"
done
and another bash file (torunR.sh)
R CMD BATCH script.R
The problem is that I don't know how to read a different "chr_X.txt" files in R (script.R).
I have tried chr_$ or chr_*', for example:
geno = read.table(file="chr_*.txt") but it didn't work.
Any ideas?? Thanks!!

Answer 1

I'm not an expert in bash scripting so I don't know the necessity of batching, but I would modify your R script to use a command line argument created within the loop.
Your R script would look like this:
## script.R
targetFile <- commandArgs(trailingOnly = TRUE)
# optional status message
cat(sprintf("Processing file %s\n", targetFile))
geno <- read.table(file = targetFile)
Then modify your bash script to be something along the lines of
#!/bin/bash
for chr in {1..23}; do \
Rscript script.R "chr_$chr.txt"
done
Result when running bash script (with optional status message):
$ ./bashScript.sh
Processing file chr_1.txt
Processing file chr_2.txt
Processing file chr_3.txt
Processing file chr_4.txt
Processing file chr_5.txt
Processing file chr_6.txt
Processing file chr_7.txt
Processing file chr_8.txt
Processing file chr_9.txt
Processing file chr_10.txt
Processing file chr_11.txt
Processing file chr_12.txt
Processing file chr_13.txt
Processing file chr_14.txt
Processing file chr_15.txt
Processing file chr_16.txt
Processing file chr_17.txt
Processing file chr_18.txt
Processing file chr_19.txt
Processing file chr_20.txt
Processing file chr_21.txt
Processing file chr_22.txt
Processing file chr_23.txt