diff options
Diffstat (limited to 'scripts/rqtl_wrapper.R')
| -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) +} |