segPairTable {genoset} | R Documentation

## Convert Rle objects to tables of segments

### 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)

[Package genoset version 1.38.0 Index]