Fix Issue #103 re read.cross.csvs with just id as phenotype

kbroman · Sep 18, 2023 · 1f4da07 · 1f4da07
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl
-Version: 1.61-1
-Date: 2023-07-15
+Version: 1.61-2
+Date: 2023-09-19
 Title: Tools for Analyzing QTL Experiments
 Author: Karl W Broman <broman@wisc.edu> and Hao Wu, with
   ideas from Gary Churchill and Saunak Sen and contributions from

diff --git a/NEWS.md b/NEWS.md
@@ -1,12 +1,15 @@
 # Revision history for the R/qtl package
 
-## Version 1.61, 2023-07-15
+## Version 1.61, 2023-09-19
 
 ### Bug fixes
 
 - Fixed bug in `summary.scanone()` for the case `format="onepheno"` but
   `threshold` has length > 1. (Issue #102.)
 
+- Fixed bug in `read.cross()` for format `"csvs"` when the phenotype
+  file contains only the identifiers. (Issue #103.)
+
 
 ## Version 1.60, 2023-04-18
 

diff --git a/R/read.cross.csvs.R b/R/read.cross.csvs.R
@@ -196,9 +196,11 @@ read.cross.csvs <-
     else
         map <- rep(0,ncol(gen))
 
-    colnames(pheno) <- unlist(pheno[1,])
+    colnames_pheno <- unlist(pheno[1,])
+
     pheno <- apply(pheno, 2, function(a) { a[!is.na(a) & a==""] <- NA; a })
     pheno <- as.data.frame(pheno[-1,], stringsAsFactors=TRUE)
+    colnames(pheno) <- colnames_pheno
 
     # replace empty cells with NA
     gen <- sapply(gen,function(a) { a[!is.na(a) & a==""] <- NA; a })