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Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 13 |
1 files changed, 6 insertions, 7 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index c3f6932..a4fcbfb 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -496,18 +496,17 @@ covar <- NULL covar - -# TODO fix this hardcoded chromosome -# TODO get all chromosomes and iterate coeff_results for a given chromosomes -coeff_results <- get_qtl_effect("5", Pr, pheno) - meffects <- c() # TODO add plots for meffects - for (chr in chr_names(dataset)){ cat("Getting the qtl effect for chromosome", chr) cat("\n") - coeff_results <- get_qtl_effect(chr, Pr, pheno) + if (dataset$crosstype == "4way"){ + coeff_results <- get_qtl_effect(chr, aPr, pheno, LOCO="LOCO", covar = sex) + } else { + coeff_results <- get_qtl_effect(chr, Pr, pheno) + } + meffects <- append(meffects, coeff_results) } |