WGBSseg: Copy number segmentation of GC- & mapping-corrected WGBS...

In ttriche/biscuitEater: a bunch of convenience functions for Biscuit

Description

FIXME: use some form of smoothing to glob segments together and THEN filter on length (as opposed to right now where it is done rather roughly) FIXME: use findOverlaps(resize(segs, width(segs) + minWidth, fix="center"))

Usage

WGBSseg(cn, minAbs = 0.3, minWidth = 20000, ...)

Arguments

cn	binned, corrected read depths from correctCoverage()
minAbs	minimum absolute value of a segment to keep it (0.1)
minWidth	minimum width of segment (NOT A GAP) to keep (25000)
...	other parameters passed to fastseg

Value

         a GRanges (hg19 seqinfo)

Examples

  library(fastseg)
  library(HMMcopy) 
  library(rtracklayer)
  files <- list.files(patt="P01-022-.*covg.hg19.bw") 
  names(files) <- sapply(strsplit(files, "(\\.|\\-)"), `[`, 3)
  covgs <- sapply(files, import)

  RMS1 <- correctBsSeqCoverage(covgs$tumor1, covgs$normal)
  RMS1seg <- WGBSseg(RMS1)
  plotSegs(RMS1, RMS1seg, "chr10")

  RMS2 <- correctBsSeqCoverage(covgs$tumor2, covgs$normal)
  RMS2seg <- WGBSseg(RMS2) 
  plotSegs(RMS2, RMS2seg, "chr10")

ttriche/biscuitEater documentation built on May 15, 2019, 4:18 p.m.