diff options
| -rw-r--r-- | scripts/rqtl_wrapper.R | 10 |
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(...) } |