segTable-methods: Convert Rle objects to tables of segments

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Like the inverse of segs2Rle and segs2RleDataFrame. Takes a Rle or a RleDataFrame and the rowRanges both from a GenoSet object and makes a list of data.frames each like the result of CBS's segment. Note the loc.start and loc.stop will correspond exactly to probe locations in rowRanges and the input to segs2RleDataFrame are not necessarily so. 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

segTable(object, ...)

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

## S4 method for signature 'DataFrame'
segTable(object, locs, factor.chr = TRUE,
  stack = FALSE)

Arguments

object	Rle or RleDataFrame
...	in generic, for extra args in 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, segPairTable, segs2Granges, segs2RleDataFrame, segs2Rle

Examples

  data(genoset,package='genoset')
  seg.list = runCBS( genoset.ds[, , 'lrr'], rowRanges(genoset.ds), return.segs=TRUE )
  df = segs2RleDataFrame( seg.list, rowRanges(genoset.ds) )  # Loop segs2Rle on list of data.frames in seg.list
  genoset.ds[ , , 'lrr.segs'] = df
  segTable( df, rowRanges(genoset.ds) )
  segTable( genoset.ds[ , , 'lrr.segs'], rowRanges(genoset.ds) )
  segTable( genoset.ds[ , 1, 'lrr.segs'], rowRanges(genoset.ds), colnames(genoset.ds)[1] )

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