TN_WGBS_CNA: Matched tumor-normal coverage processing & segmentation

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

Description

Matched tumor-normal coverage processing & segmentation

Usage

TN_WGBS_CNA(stub0, stub1 = NULL, bsgc = NULL, maps = NULL, ...)

Arguments

stub0	bigWig stub for normal: paste0(stub0, ".covg.hg19.bw")
stub1	bigWig stub for tumor: paste0(stub1, ".covg.hg19.bw") NULL
bsgc	binned c2t GC content (default is bsgc.hg19, 1k bins) NULL
maps	binned c2t mappability (default is maps.hg19, 1k bins)NULL
...	other parameters passed to WGBSseg

Value

     a GRanges

Examples

  stubs <- c("P01-010", "P01-012", "P01-015", "P01-016", "P01-017")
  stubs <- c(stubs, "P01-018", "P01-020", "P01-021")
  names(stubs) <- paste0(stubs, "-T06-T-P01")
  names(stubs)[1] <- "P01-010-T07-T-P01"
  segs <- list()
  for(i in names(stubs)) segs[[i]] <- TN_WGBS_CNA(stubs[[i]])$segs # robust
  segs <- GRangesList(segs) # to feed to grToSeg and get full .seg output
  for(i in names(segs)) export(segs[[i]], paste0(i, ".CN.hg19.bw"))

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