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| author | zsloan | 2021-08-02 21:07:52 +0000 |
|---|---|---|
| committer | zsloan | 2021-09-23 19:29:59 +0000 |
| commit | 2cb18bb7916e029d3aa7779df710c1d0cbc910f8 (patch) | |
| tree | f9c6995b70c675d4c67a8a0f8b63d9f620a8323a | |
| parent | 72ed7dfc45bb2a1303b900c8bc5b8ddd9e189a27 (diff) | |
| download | genenetwork3-2cb18bb7916e029d3aa7779df710c1d0cbc910f8.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.R | 4 |
1 files changed, 3 insertions, 1 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index ebd5a91..ffff5b9 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -157,7 +157,7 @@ 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') @@ -246,7 +246,9 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){ 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) } |