segPairTable-methods: Convert Rle objects to tables of segments

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Like segTable, but for two Rle objects. Takes a pair of Rle or DataFrames with Rle columns and makes one or more data.frames with bounds of each new segment. Rle objects are broken up so that each resulting segment has one value from each Rle. For a DataFrame, the argument stack combines all of the individual data.frames into one large data.frame and adds a 'Sample' column of sample ids.

Usage

segPairTable(x, y, ...)

## S4 method for signature 'Rle,Rle'
segPairTable(x, y, locs = NULL, chr.ind = NULL,
  start = NULL, end = NULL, factor.chr = TRUE)

## S4 method for signature 'DataFrame,DataFrame'
segPairTable(x, y, locs, stack = FALSE,
  factor.chr = TRUE)

Arguments

x	Rle or list/DataFrame of Rle vectors
y	Rle or list/DataFrame of Rle vectors
...	in generic, extra arguments for methods
locs	GenomicRanges with rows corresponding to rows of df
chr.ind	matrix, like from chrIndices method
start	integer, vector of feature start positions
end	integer, vector of feature end positions
factor.chr	scalar logical, make 'chrom' column a factor?
stack	logical, rbind list of segment tables for each sample and add 'Sample' column?

Details

For a Rle, the user can provide locs or chr.ind, start and stop. The latter is surprisingly much faster and this is used in the DataFrame version.

Value

one or a list of data.frames with columns chrom, loc.start, loc.end, num.mark, seg.mean

See Also

Other 'segmented data': bounds2Rle, rangeSegMeanLength, runCBS, segTable, segs2Granges, segs2RleDataFrame, segs2Rle

Examples

  cn = Rle(c(3,4,5,6),rep(3,4))
  loh = Rle(c(2,4,6,8,10,12),rep(2,6))
  start = c(9:11,4:9,15:17)
  end = start
  locs = GRanges(IRanges(start=start,end=end),seqnames=c(rep('chr1',3),rep('chr2',6),rep('chr3',3)))
  segPairTable(cn,loh,locs)

genoset documentation built on Nov. 8, 2020, 6:07 p.m.