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| author | zsloan | 2021-07-23 20:08:36 +0000 |
|---|---|---|
| committer | zsloan | 2021-07-23 20:08:36 +0000 |
| commit | b3e6105b5d8d2c2f30f2609290ef62fa17f32e62 (patch) | |
| tree | d3831cf122f3b510401951a7149fb34c5c39f96b | |
| parent | c3d59414b4bd23e52823a8b7e846f732e36d8c56 (diff) | |
| download | genenetwork3-b3e6105b5d8d2c2f30f2609290ef62fa17f32e62.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 77ed227..d8ecfaa 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -158,7 +158,7 @@ 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) @@ -244,4 +244,9 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){ qtl_results = scan_func(cross_object, pheno.col=1, model=opt$model, method=opt$method) } -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) +} |