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authorzsloan2022-02-02 20:10:00 +0000
committerzsloan2022-02-02 14:15:25 -0600
commit750bc975650d27e67d1d0b3f6ecaab6582304b44 (patch)
treec35ef02507b42e89287e0f9761ba46baf3768135
parent9ac9e6a305e5e96d24a67a7469e3f2ea66fc0c72 (diff)
downloadgenenetwork3-750bc975650d27e67d1d0b3f6ecaab6582304b44.tar.gz
Fix R/qtl covar bug
The rqtl_wrapper script was throwing an error when only a single categorical covariate was used. This is apparently because "covars[,name]" throws an error in such a situation. Using just "covars" in such a situation prevents the error. So I just added an if statement checking the number of covariates. There might be some better way to deal with this in R, but this is the best I could come up with.
-rw-r--r--scripts/rqtl_wrapper.R13
1 files changed, 9 insertions, 4 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index b7a9ae0..13c2684 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -202,14 +202,19 @@ if (!is.null(opt$addcovar)) {
name <- paste0("T_", covarDescr[x, 1]) # The covar description file doesn't have T_ in trait names (the cross object does)
type <- covarDescr[x, 2]
if(type == "categorical"){
- if(length(table(covars[,name])) > 2){ # More then 2 levels create the model matrix for the factor
- mdata <- data.frame(toExpand = as.factor(covars[, name]))
+ verbose_print('Binding covars to covars\n')
+ if (nrow(covarDescr) < 2){
+ this_covar = covars
+ } else {
+ this_covar = covars[,name]
+ }
+ if(length(table(this_covar)) > 2){ # More then 2 levels create the model matrix for the factor
+ mdata <- data.frame(toExpand = as.factor(this_covar))
options(na.action='na.pass')
modelmatrix <- model.matrix(~ toExpand + 0, mdata)[,-1]
covars <- cbind(covars, modelmatrix)
}else{ # 2 levels? just bind the trait as covar
- verbose_print('Binding covars to covars\n')
- covars <- cbind(covars, covars[,name])
+ covars <- cbind(covars, this_covar)
}
}
}