diff options
Diffstat (limited to 'scripts/rqtl_wrapper.R')
| -rw-r--r-- | scripts/rqtl_wrapper.R | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index f7e0406..7518175 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -167,7 +167,7 @@ if (!is.null(opt$addcovar)) { if (!is.null(opt$pstrata)) { covar_names = trait_names[3:length(trait_names) - 1] } else { - covar_names = trait_names[3:length(trait_names)] + covar_names = trait_names[2:length(trait_names)] } covars <- pull.pheno(cross_object, covar_names) } @@ -195,18 +195,18 @@ if (opt$nperm > 0) { if (!is.null(opt$addcovar) || !is.null(opt$control)){ if (!is.null(opt$pstrata)) { - verbose_print('Running permutations with cofactors and strata\n') + verbose_print('Running ', opt$nperm, ' permutations with cofactors and strata\n') perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method) } else { - verbose_print('Running permutations with cofactors\n') + verbose_print('Running ', opt$nperm, ' permutations with cofactors\n') perm_results = scanone(cross_object, pheno.col=1, addcovar=covars, n.perm=opt$nperm, model=opt$model, method=opt$method) } } else { if (!is.null(opt$pstrata)) { - verbose_print('Running permutations with strata\n') + verbose_print('Running ', opt$nperm, ' permutations with strata\n') perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, perm.strata=perm_strata, model=opt$model, method=opt$method) } else { - verbose_print('Running permutations\n') + verbose_print('Running ', opt$nperm, ' permutations\n') perm_results = scanone(cross_object, pheno.col=1, n.perm=opt$nperm, model=opt$model, method=opt$method) } } |