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Viewing changes to R/RangedData-methods.R

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-10-18 10:40:04 UTC
  • Revision ID: package-import@ubuntu.com-20131018104004-ktm4ub0pcoybnir6
Tags: upstream-1.12.4
Import upstream version 1.12.4

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R/RangedData-methods.R
 
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### =========================================================================
 
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### RangedData/RangesList implementation of the GenomicRanges API
 
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### -------------------------------------------------------------------------
 
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###
 
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
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### seqinfo
 
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###
 
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setMethod("seqinfo", "List", function(x) {
 
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  si <- metadata(x)$seqinfo
 
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  if (is.null(si)) {
 
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    sn <- names(x)
 
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    if (is.null(sn))
 
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      sn <- as.character(seq(length(x)))
 
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    si <- Seqinfo(unique(sn))
 
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  }
 
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  si  
 
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})
 
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setMethod("seqinfo", "RangesList", function(x) {
 
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  si <- callNextMethod()
 
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  if (!is.null(universe(x)))
 
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    genome(si) <- universe(x)
 
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  si
 
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})
 
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### FIXME: needs sanity checks
 
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setReplaceMethod("seqinfo", "List",
 
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                 function(x, value) {
 
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                   metadata(x)$seqinfo <- value
 
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                   x
 
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                 })
 
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setMethod("seqinfo", "RangedData", function(x) seqinfo(ranges(x)))
 
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setReplaceMethod("seqinfo", "RangedData",
 
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                 function(x, value) {
 
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                   seqinfo(ranges(x)) <- value
 
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                   x
 
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                 })
 
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
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### seqnames
 
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###
 
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setMethod("seqnames", "RangesList", function(x) {
 
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  if (is.null(names(x)))
 
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    NULL
 
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  else seqsplit(Rle(space(x)), rep(names(x), elementLengths(x)))
 
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})
 
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setMethod("seqnames", "RangedData", function(x) space(x))
 
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