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authorzsloan2021-07-23 20:08:36 +0000
committerzsloan2022-03-22 19:07:00 +0000
commitacfea0fc8793372723be0e64316002ed9bc2403b (patch)
tree0fb3533a0663126bb53c948221eead6794df499d /scripts/rqtl_wrapper.R
parent2849792ddc2e76750421c75d926d5a7f18c57e97 (diff)
downloadgenenetwork3-acfea0fc8793372723be0e64316002ed9bc2403b.tar.gz
Added line priting pair-scan results to CSV and changed the default step-size to 10cM for pair-scan
Diffstat (limited to 'scripts/rqtl_wrapper.R')
-rw-r--r--scripts/rqtl_wrapper.R9
1 files changed, 7 insertions, 2 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index 0d13ccb..26d0a9c 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -177,7 +177,7 @@ if (!is.null(opt$interval)) {
cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max")
} else if (!is.null(opt$pairscan)) {
verbose_print('Calculating genotype probabilities with interval mapping\n')
- cross_object <- calc.genoprob(cross_object, step=20)
+ cross_object <- calc.genoprob(cross_object, step=10)
} else {
verbose_print('Calculating genotype probabilities\n')
cross_object <- calc.genoprob(cross_object)
@@ -338,4 +338,9 @@ if (type == "4-way") {
colnames(qtl_results)[4:7] <- c("AC", "AD", "BC", "BD")
}
-write.csv(qtl_results, out_file)
+verbose_print('Writing results to CSV file\n')
+if (!is.null(opt$pairscan)) {
+ write.csv(qtl_results[1], out_file)
+} else {
+ write.csv(qtl_results, out_file)
+}