aboutsummaryrefslogtreecommitdiff
path: root/scripts/rqtl_wrapper.R
diff options
context:
space:
mode:
authorzsloan2021-10-14 21:00:15 +0000
committerzsloan2021-10-14 21:00:15 +0000
commit77099cac68e8f4792bf54d8e1f7ce6f315bedfa7 (patch)
tree26e241390bb1209032576397f7c1780471b99f92 /scripts/rqtl_wrapper.R
parentbaa801e81c5b0f7c7b30c6ca880a806a6bce54db (diff)
downloadgenenetwork3-77099cac68e8f4792bf54d8e1f7ce6f315bedfa7.tar.gz
Fixed when model is set to account for situations with no covariates
Diffstat (limited to 'scripts/rqtl_wrapper.R')
-rw-r--r--scripts/rqtl_wrapper.R6
1 files changed, 5 insertions, 1 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index 523888f..b7a9ae0 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -300,7 +300,11 @@ if (type == "4-way") {
traitname <- colnames(pull.pheno(cross_object))[1]
gtsp <- pull.genoprob(cross_object)
allpheno <- pull.pheno(cross_object)
- model <- paste0(traitname, " ~ ", paste0(covar_names, sep="", collapse=" + "))
+ if (!is.null(opt$addcovar)) {
+ model <- paste0(traitname, " ~ ", paste0(covar_names, sep="", collapse=" + "))
+ } else {
+ model <- paste0(traitname, " ~ 1 ")
+ }
meffects <- c()
verbose_print("Getting QTL main effects for 4-way crosses")