diff options
| -rw-r--r-- | scripts/rqtl_wrapper.R | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index fd786cf..31c1277 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -262,9 +262,9 @@ if (!is.null(opt$pairscan)) { # Calculate permutations if (opt$nperm > 0) { if (!is.null(opt$filename)){ - perm_out_file = file.path(opt$outdir, "output", paste("PERM_", opt$filename, sep = "" )) + perm_out_file = file.path(opt$outdir, "gn3", paste("PERM_", opt$filename, sep = "" )) } else { - perm_out_file = file.path(opt$outdir, "output", paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = "")) + perm_out_file = file.path(opt$outdir, "gn3", paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = "")) } if (!is.null(opt$addcovar) || !is.null(opt$control)){ @@ -303,7 +303,7 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){ verbose_print('Writing results to CSV file\n') if (!is.null(opt$pairscan)) { - map_out_file = file.path(opt$outdir, "output", paste("MAP_", opt$filename, sep = "" )) + map_out_file = file.path(opt$outdir, "gn3", paste("MAP_", opt$filename, sep = "" )) write.csv(qtl_results[1], out_file) write.csv(qtl_results[2], map_out_file) } else { |