run.meta.unit

#!/usr/bin/env Rscript
library(GMMAT)
library(data.table)
## Expects : a variant set file and a set of directories
argv = commandArgs(trailingOnly = TRUE)
outdir=argv[1]
argv=argv[-1]
group_file=argv[1]
argv=argv[-1]

cohorts=basename(argv)
if(length(cohorts)<2){stop("ERROR : only one cohort.")}
cohorts=tstrsplit(cohorts, ".", fixed=T)[[1]]

trait=basename(argv[1])
trait=sub(paste0(cohorts[1], "."), "", trait)
trait=sub(".out", "",trait)
cat(paste("INFO: Detected trait", trait, "\n"))

nfiles=length(list.files(dirname(argv[1]), pattern=paste0(basename(argv[1]), ".score.*")))
for(i in 2:length(argv)){
  if(nfiles != length(list.files(dirname(argv[i]), pattern=paste0(basename(argv[i]), ".score.*")))){
    stop(paste("ERROR : Cohort", cohorts[i], "has",  length(list.files(dirname(argv[i]), pattern=paste0(basename(argv[i]), ".score.*"))),
  "files, expected", nfiles))}
}

cat(paste("INFO: Meta-analysing", nfiles, "files\n"))

meta=SMMAT.meta(meta.files.prefix=argv, n.files=rep(nfiles, length(cohorts)),
        group.file=group_file,
        MAF.range=c(1e-10, 0.05),
        MAF.weights.beta = c(1,1),
        miss.cutoff=0.01,
        tests=c("O", "E"),
        rho=(0:10)/10,
        use.minor.allele=T
          )
ofn=paste(outdir, paste(paste(cohorts, collapse="."), trait, "out", sep="."), sep="/")
fwrite(meta, ofn, sep="\t", na=NA, quote=F)