Revise cross2_to_grcm39 to consider GM/MM combination (Issue rqtl#6)

kbroman · Mar 17, 2023 · 2da7a37 · 2da7a37
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: mmconvert
-Version: 0.3-2
+Version: 0.3-3
 Date: 2023-03-17
 Title: Mouse Map Converter
 Description: Function to convert mouse genome positions between the build 39 physical map and the Cox genetic map <doi:10.1534/genetics.109.105486>.

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,13 @@
-## mmconvert 0.3-2 (2023-03-17)
+## mmconvert 0.3-3 (2023-03-17)
 
 - Revised Cox genetic maps, estimated using the original crimap software.
 
 - Revised MUGAmaps, using the corrected Cox genetic maps.
 
+- Revised `cross2_to_grcm39()` so that it will also consider that
+  markers are from the combination of GigaMUGA and MegaMUGA arrays
+  (Issue #6).
+
 
 ## mmconvert 0.2-4 (2021-10-13)
 

diff --git a/R/cross2_to_grcm39.R b/R/cross2_to_grcm39.R
@@ -46,6 +46,14 @@ cross2_to_grcm39 <-
         # compare marker names to the four MUGA arrays
         # use the one with the most matches
 
+        # include the combination of GM and MM
+        muga_maps$gm_n_mm <- rbind(muga_maps$gm, muga_maps$mm[!(muga_maps$mm$marker %in% muga_maps$gm$marker),])
+        muga_maps$gm_n_mm <- muga_maps$gm_n_mm[order( factor(muga_maps$gm_n_mm$chr, c(1:19,"X")),
+                                                     muga_maps$gm_n_mm$bp_grcm39,
+                                                     muga_maps$gm_n_mm$cM_cox,
+                                                     muga_maps$gm_n_mm$marker), ]
+
+
         n_match <- vapply(muga_maps, function(a,b) sum(b %in% a$marker), 0, markers)
         if(!any(n_match > 0)) {
             stop("No markers found in the MUGA arrays")