Description Usage Arguments Value Examples
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"))
1 |
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 |
1 | a GRanges (hg19 seqinfo)
|
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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")
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