runCBS: Run CBS Segmentation

Description Usage Arguments Details Value See Also Examples

View source: R/segments.R

Description

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

Usage

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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

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    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

genoset documentation built on Nov. 17, 2017, 9:22 a.m.