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authorzsloan2021-08-02 21:07:52 +0000
committerzsloan2022-03-22 19:08:01 +0000
commit4c3359082fbb1eef93a9e54c633f938606cba5f6 (patch)
treeee540fd6bc5c92cb90693616d7bc6a6a5f5a9ee3
parent444095309a8841a0998e74f2f4eba2c3fea6890f (diff)
downloadgenenetwork3-4c3359082fbb1eef93a9e54c633f938606cba5f6.tar.gz
Updated rqtl_wrapper to also return a map file when doing a pair-scan (since we need the list of markers/pseudomarkers and their positions)
-rw-r--r--scripts/rqtl_wrapper.R4
1 files changed, 3 insertions, 1 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index 26d0a9c..fb12012 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -176,7 +176,7 @@ if (!is.null(opt$interval)) {
verbose_print('Calculating genotype probabilities with interval mapping\n')
cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max")
} else if (!is.null(opt$pairscan)) {
- verbose_print('Calculating genotype probabilities with interval mapping\n')
+ verbose_print('Calculating genotype probabilities for pair-scan\n')
cross_object <- calc.genoprob(cross_object, step=10)
} else {
verbose_print('Calculating genotype probabilities\n')
@@ -340,7 +340,9 @@ if (type == "4-way") {
verbose_print('Writing results to CSV file\n')
if (!is.null(opt$pairscan)) {
+ map_out_file = file.path(opt$outdir, paste("MAP_", opt$filename, sep = "" ))
write.csv(qtl_results[1], out_file)
+ write.csv(qtl_results[2], map_out_file)
} else {
write.csv(qtl_results, out_file)
}