genoprob_to_snpprob: revise to work with DOF1 and HSF1

- Fixes Issue rqtl#140 (I thin)
kbroman · Oct 28, 2022 · 12a9266 · 12a9266
1 parent cfb0e0d
commit 12a9266
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/R/snpprob_from_cross.R b/R/snpprob_from_cross.R
@@ -25,6 +25,10 @@ snpprob_from_cross <-
     map <- cross$pmap
     if(is.null(map)) map <- cross$gmap
 
+    if(cross$crosstype %in% c("hsf1", "dof1")) { # if HSF1 or DOF1, drop last founder
+        cross$founder_geno <- cross$founder_geno[,-ncol(cross$founder_geno)]
+    }
+
     sdp <- calc_sdp(t(do.call("cbind", cross$founder_geno)))
 
     snpinfo <- data.frame(chr=rep(chr_names(cross), n_mar(cross)),