find_dup_markers: need to include founder_geno, if available

kbroman · Nov 10, 2023 · 4ff007c · 4ff007c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: qtl2
-Version: 0.33-4
+Version: 0.33-5
 Date: 2023-11-10
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: Provides a set of tools to perform quantitative

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-## qtl2 0.33-4 (2023-11-10)
+## qtl2 0.33-5 (2023-11-10)
 
 ### Major changes
 

diff --git a/R/find_dup_markers.R b/R/find_dup_markers.R
@@ -52,7 +52,13 @@ find_dup_markers <-
     if(!is.cross2(cross))
         stop('Input cross should be a "cross2" object.')
 
+    # genotypes as one matrix; include founder_geno
+
     g <- do.call("cbind", cross$geno)
+    if(!is.null(cross$founder_geno)) {
+        g <- rbind(g, do.call("cbind", cross$founder_geno))
+    }
+
     markers <- colnames(g)
     markerloc <- lapply(n_mar(cross), function(a) 1:a)
     if(length(markerloc) > 1) {