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Bugfix: Do not use countInvalidList to filter uniqueChr
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* This line was giving bizarre regions for chrM that shouldn't have
existed because countInvalidList was way longer than uniqueChr.
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rcavalcante committed Dec 17, 2015
1 parent 508b3e4 commit aa0eb22
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Showing 2 changed files with 4 additions and 5 deletions.
6 changes: 3 additions & 3 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: methylSig
Type: Package
Title: a whole genome DNA methylation analysis pipeline
Version: 0.4.0
Date: 2015-12-16
Version: 0.4.1
Date: 2015-12-17
Author: Yongseok Park
Maintainer: Who to complain to <[email protected]>
Description: MethylSig is a method for testing for differentially methylated
Expand All @@ -28,6 +28,6 @@ Suggests:
testthat,
knitr,
rmarkdown
Packaged: 2015-12-16; rcavalca
Packaged: 2015-12-17; rcavalca
VignetteBuilder: knitr
RoxygenNote: 5.0.1
3 changes: 1 addition & 2 deletions R/read.R
Original file line number Diff line number Diff line change
Expand Up @@ -172,8 +172,7 @@ methylSigReadData = function(fileList,
((coverage[, fileIndex] != 0) & (coverage[, fileIndex] < minCount)) |
((coverage[, fileIndex] != 0) & (coverage[, fileIndex] > maxCount)) ) ) )
}

uniqueChr = uniqueChr[-countInvalidList]

uniqueLoc = uniqueLoc[-countInvalidList]
strand = strand[-countInvalidList]
coverage = coverage[-countInvalidList, ]
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