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fixing problem in orderBSseq related to seqOrder and seqnames(BSseq)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@78189 bc3139a8-67e5-0310-9ffc-ced21a209358

khansen authored on 09/07/2013 01:30:03
Showing 3 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 0.9.4
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+Version: 0.9.5
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: Tools for analyzing and visualizing bisulfite sequencing data
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 Author: Kasper Daniel Hansen
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@@ -37,7 +37,7 @@ orderBSseq <- function(BSseq, seqOrder = NULL) {
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     if(is.null(seqOrder))
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         seqOrder <- names(splitNames)
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     else
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-        stopifnot(all(seqOrder %in% names(splitNames)))
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+        seqOrder <- seqOrder[seqOrder %in% names(splitNames)]
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     splitOd <- lapply(seqOrder, function(nam) {
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         seqRanges <- seqselect(ranges(granges(BSseq)), splitNames[[nam]]) 
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         as.integer(unlist(splitNames[[nam]])[order(start(seqRanges))])
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@@ -14,6 +14,7 @@
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     completely. The new class is build on 'SummarizedExperiment' from
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     GenomicRanges instead of 'hasGRanges'.  Use 'x <- updateObject(x)' to
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     update serialized (saved) objects.
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+    \item Fixing a problem in orderBSseq related to chromosome names.
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   }
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 }
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