From 750bc975650d27e67d1d0b3f6ecaab6582304b44 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 2 Feb 2022 20:10:00 +0000
Subject: 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.
---
 scripts/rqtl_wrapper.R | 13 +++++++++----
 1 file 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)
       }
     }
   }
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