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authorzsloan2021-08-28 00:47:39 +0000
committerzsloan2021-08-28 00:47:39 +0000
commit79d19f4ce5cdce7f78128e8d7321dfa701e1d04b (patch)
tree527e36b9c906d5e41e858744c98f95d7fdd5de33 /scripts/rqtl_wrapper.R
parent14d0a6649f6ecbb374a24f37efcd3a73982cf4c2 (diff)
downloadgenenetwork3-79d19f4ce5cdce7f78128e8d7321dfa701e1d04b.tar.gz
Fix issue that caused R/qtl to not use the first covariate when using stratified permutations + covariates
Diffstat (limited to 'scripts/rqtl_wrapper.R')
-rw-r--r--scripts/rqtl_wrapper.R2
1 files changed, 1 insertions, 1 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index f6788c5..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)
}