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| author | zsloan | 2021-07-23 20:08:36 +0000 |
|---|---|---|
| committer | zsloan | 2022-03-22 19:07:00 +0000 |
| commit | acfea0fc8793372723be0e64316002ed9bc2403b (patch) | |
| tree | 0fb3533a0663126bb53c948221eead6794df499d | |
| parent | 2849792ddc2e76750421c75d926d5a7f18c57e97 (diff) | |
| download | genenetwork3-acfea0fc8793372723be0e64316002ed9bc2403b.tar.gz | |
Added line priting pair-scan results to CSV and changed the default step-size to 10cM for pair-scan
| -rw-r--r-- | scripts/rqtl_wrapper.R | 9 |
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) +} |