runCBS {genoset} | R Documentation

## Run CBS Segmentation

### Description

Utility function to run CBS's three functions on one or more samples

### Usage

    runCBS(data, locs, return.segs = FALSE, n.cores = 1, smooth.region = 2,
      outlier.SD.scale = 4, smooth.SD.scale = 2, trim = 0.025,
      alpha = 0.001)

### Arguments

`data` | numeric matrix with continuous data in one or more columns
`locs` | GenomicRanges, like rowRanges slot of GenoSet
`return.segs` | logical, if true list of segment data.frames return, otherwise a DataFrame of Rle vectors. One Rle per sample.
`n.cores` | numeric, number of cores to ask mclapply to use
`smooth.region` | number of positions to left and right of individual positions to consider when smoothing single point outliers
`outlier.SD.scale` | number of SD single points must exceed smooth.region to be considered an outlier
`smooth.SD.scale` | floor used to reset single point outliers
`trim` | fraction of sample to smooth
`alpha` | pvalue cutoff for calling a breakpoint

### Details

Takes care of running CBS segmentation on one or more samples. Makes appropriate input, smooths outliers, and segment

### Value

data frame of segments from CBS

### See Also

Other "segmented data": `bounds2Rle`, `rangeSegMeanLength`, `segPairTable`, `segTable`, `segs2Granges`, `segs2RleDataFrame`, `segs2Rle`

### Examples

        sample.names = paste("a",1:2,sep="")
        probe.names =  paste("p",1:30,sep="")
        ds = matrix(c(c(rep(5,20),rep(3,10)),c(rep(2,10),rep(7,10),rep(9,10))),ncol=2,dimnames=list(probe.names,sample.names))
        locs = GRanges(ranges=IRanges(start=c(1:20,1:10),width=1,names=probe.names),seqnames=paste("chr",c(rep(1,20),rep(2,10)),sep=""))

        seg.rle.result = RleDataFrame( a1 = Rle(c(rep(5,20),rep(3,10))), a2 = Rle(c(rep(2,10),rep(7,10),rep(9,10))), row.names=probe.names )
        seg.list.result = list(
          a1 = data.frame( ID=rep("a1",2), chrom=factor(c("chr1","chr2")), loc.start=c(1,1), loc.end=c(20,10), num.mark=c(20,10), seg.mean=c(5,3), stringsAsFactors=FALSE),
          a2 = data.frame( ID=rep("a2",3), chrom=factor(c("chr1","chr1","chr2")), loc.start=c(1,11,1), loc.end=c(10,20,10), num.mark=c(10,10,10), seg.mean=c(2,7,9), stringsAsFactors=FALSE)
          )

        runCBS(ds,locs)  # Should give seg.rle.result
        runCBS(ds,locs,return.segs=TRUE) # Should give seg.list.result

[Package genoset version 1.38.0 Index]