Minor bugfix in methylSigTile()

Cannot reproduce everywhere, but sometimes when a chromosome has no entries in the meth object, the tiling function failed. Now check for entries on the chromosome.
sartorlab · Jan 25, 2019 · 63a015d · 63a015d
1 parent 897d0ae
commit 63a015d
Show file tree

Hide file tree

Showing 3 changed files with 15 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: methylSig
 Type: Package
 Title: a whole genome DNA methylation analysis pipeline
-Version: 0.5.0
-Date: 2018-12-05
+Version: 0.5.1
+Date: 2019-01-25
 Authors@R: c(
     person("Yongseok", "Park", email = "[email protected]", role = c("aut")),
     person("Raymond G.", "Cavalcante", email = "[email protected]", role = c("aut", "cre")))

diff --git a/NEWS b/NEWS
@@ -1,3 +1,10 @@
+CHANGES IN VERSION 0.5.1
+------------------------
+
+    o Minor bugfix in methylSigTile() function. Cannot reproduce everywhere,
+      but sometimes when a chromosome has no entries in the meth object, the
+      tiling function failed. Now check for entries on the chromosome.
+
 CHANGES IN VERSION 0.5.0
 ------------------------
 

diff --git a/R/tile.R b/R/tile.R
@@ -32,10 +32,12 @@ methylSigTile <- function(meth, tiles = NULL, win.size = 200) {
         )
         seqinfo_list = split(seqinfo_df, seqinfo_df$seqnames)
         seqinfo_list = lapply(seqinfo_list, function(chr){
-            max_df = data.frame(
-                seqnames = unique(chr$seqnames),
-                end = max(chr$end)
-            )
+            if(nrow(chr) > 0) {
+                max_df = data.frame(
+                    seqnames = unique(chr$seqnames),
+                    end = max(chr$end)
+                )
+            }
         })
         seqinfo_df = Reduce(rbind, seqinfo_list)