How to resolve the warning message in detectRUNS on R software

Question

[taniamahmood38]

Hi,

I am using detectRUNS package on R software to visualize my roh data generated by bcftools roh option. I used these commands on R but the second command gives a warning message

savedRunFile <- system.file("extdata", "input_roh.txt", package="BCFtools")
runs <- readExternalRuns(inputFile = savedRunFile, program = "BCFtools")
Loading file from BCFtools
Warning message:
In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former

Kindly guide me about the warning message. I am a novice to R and don't know what exactly this warning line is and how to resolve the issue. Any help is highly appreciated.

Thanks in advance

Answer 1

[rpolicastro]

Your system.file command is telling R to look for the input_roh.txt file within the BCFtools library folder, which you probably didn't mean to do. Try changing the inputFile argument of readExternalRuns to that file name instead. This assumes the file is in the working directory of R, if not you need to include a relative or absolute path to it.

[taniamahmood38]

Many thanks for helping me out.