Fix issue #102 re vector-valued threshold in summary.scanone()

kbroman · Jul 15, 2023 · 1acfc04 · 1acfc04
1 parent ab92398
commit 1acfc04
Show file tree

Hide file tree

Showing 3 changed files with 16 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl
-Version: 1.60
-Date: 2023-04-18
+Version: 1.61-1
+Date: 2023-07-15
 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
@@ -1,5 +1,13 @@
 # Revision history for the R/qtl package
 
+## Version 1.61, 2023-07-15
+
+### Bug fixes
+
+- Fixed bug in `summary.scanone()` for the case `format="onepheno"` but
+  `threshold` has length > 1. (Issue #102.)
+
+
 ## Version 1.60, 2023-04-18
 
 ### Minor changes

diff --git a/R/summary.scanone.R b/R/summary.scanone.R
@@ -158,8 +158,13 @@ summary.scanone <-
         }
         thechr <- as.character(object[wh,1])
 
-        if(!missing(threshold))
+        if(!missing(threshold)) {
+            if(length(threshold) > 1) {
+                warning('when format="allpheno", threshold should have length 1')
+                threshold <- threshold[1]
+            }
             wh <- wh[object[wh,lodcolumn] > threshold]
+        }
         else if(!missing(alpha)) {
             thr <- summary(perms, alpha)
             if("xchr" %in% names(attributes(perms))) {