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authorzsloan2022-03-22 20:28:58 +0000
committerzsloan2022-03-22 20:28:58 +0000
commit0e6990940e22eb0431d6a27e45d29bc04d8ad582 (patch)
tree921ee8b592ad4850b13dab48ab6793be8fe9ef3c
parent47c38fe08f27a7de58430c2f7f5635a9ba5836c8 (diff)
downloadgenenetwork3-0e6990940e22eb0431d6a27e45d29bc04d8ad582.tar.gz
Change order of if statements for running genoprob command
Now it checks for pairscan first, just in case interval ends up being passed (which is an irrelevant parameter for pairscan) Also added a couple more verbose prints
-rw-r--r--scripts/rqtl_wrapper.R10
1 files changed, 6 insertions, 4 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index fb12012..5ecd774 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -172,12 +172,12 @@ verbose_print('Generating cross object\n')
cross_object = geno_to_csvr(geno_file, trait_names, trait_vals, cross_file, type)
# Calculate genotype probabilities
-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)) {
+if (!is.null(opt$pairscan)) {
verbose_print('Calculating genotype probabilities for pair-scan\n')
cross_object <- calc.genoprob(cross_object, step=10)
+} else if (!is.null(opt$interval)) {
+ verbose_print('Calculating genotype probabilities with interval mapping\n')
+ cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max")
} else {
verbose_print('Calculating genotype probabilities\n')
cross_object <- calc.genoprob(cross_object)
@@ -241,10 +241,12 @@ if (!is.null(opt$control)) {
}
if (!is.null(opt$pairscan)) {
+ verbose_print("Running scantwo")
scan_func <- function(...){
scantwo(...)
}
} else {
+ verbose_print("Running scanone")
scan_func <- function(...){
scanone(...)
}