Fix bug in addint and addcovarint re X chr QTL (Issue #101)

kbroman · Mar 24, 2023 · 65d4f5a · 65d4f5a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl
-Version: 1.59-1
-Date: 2023-02-18
+Version: 1.59-2
+Date: 2023-03-23
 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
@@ -1,11 +1,17 @@
 # Revision history for the R/qtl package
 
-## Version 1.59, 2023-02-18
+## Version 1.59-2, 2023-03-23
 
 ### Minor changes
 
 - In the CITATION file, change from `citEntry()` to `bibentry()`.
 
+### Bug fixes
+
+- Fixed bug in addint() and addcovarint(): when X chr QTL and missing
+  phenotypes, would halt with error because cross wasn't getting
+  subset. (Issue #101)
+
 
 ## Version 1.58, 2022-12-22
 

diff --git a/R/addqtl.R b/R/addqtl.R
@@ -2,8 +2,8 @@
 #
 # addqtl.R
 #
-# copyright (c) 2007-2021, Karl W. Broman
-# last modified Mar, 2021
+# copyright (c) 2007-2023, Karl W. Broman
+# last modified Mar, 2023
 # first written Nov, 2007
 #
 #     This program is free software; you can redistribute it and/or
@@ -133,6 +133,7 @@ addint <-
                 qtl$prob <- lapply(qtl$prob, function(a) a[!hasmissing,,drop=FALSE])
 
             if(!is.null(covar)) covar <- covar[!hasmissing,,drop=FALSE]
+            cross <- subset(cross, ind=!hasmissing)
         }
     }
 
@@ -1284,6 +1285,7 @@ addcovarint <-
                 qtl$prob <- lapply(qtl$prob, function(a) a[!hasmissing,,drop=FALSE])
 
             covar <- covar[!hasmissing,,drop=FALSE]
+            cross <- subset(cross, ind=!hasmissing)
         }
     }