Clumping stopping without error potentially due to tempfile()

[Sabor117]

Hi all,

I have recently encountered an issue when running clumping using the ieugwasr::ld_clump() function (this is using ieugwasr_0.1.5).

Rather than an issue with the ieugwasr package, I actually suspect this may be an issue with the local file system and HPC I am using and may be due to the location of where the script is saving temporary files.

I see that ld_clump() calls ld_clump_local() if you provide a local version of plink for conducting the clumping and that within this function there is the following:

fn <- tempfile()
write.table(data.frame(SNP = dat[["rsid"]], P = dat[["pval"]]), 
        file = fn, row.names = F, col.names = T, quote = F)
fun2 <- paste0(shQuote(plink_bin, type = shell), " --bfile ", 
        shQuote(bfile, type = shell), " --clump ", shQuote(fn, 
            type = shell), " --clump-p1 ", clump_p, " --clump-r2 ", 
        clump_r2, " --clump-kb ", clump_kb, " --out ", shQuote(fn, 
            type = shell))
system(fun2)

I.e. It creates a tempfile() and then this is used in --out and --clump. I wonder if it would be possible to have a version of this where you can optionally provide a tmpdir for this file, in case this is clashing with mine (and other's) file systems?