MAP.fun: Mappability calculator

In mskilab/fragCounter: GC mappability correction and segmentation

Mappability calculator

Description

Calculates mappability as fraction of bases in a tile with mappability of 1

Usage

MAP.fun(
  win.size = 200,
  twobitURL = "~/DB/UCSC/hg19.2bit",
  bw.path = "~/DB/UCSC/wgEncodeCrgMapabilityAlign100mer.bigWig",
  twobit.win = 1000,
  mc.cores = 1,
  exome = FALSE,
  chr.sub = TRUE
)

Arguments

win.size	integer Window size, in basepairs, to calculate mappability for (should match window size of your coverage file
twobitURL	string URL to twobit genome file. Default is hg19 from UCSC
bw.path	string Path to .bigWig mappability file
twobit.win	integer How many windows of the twobit file to load into memory on each core
mc.cores	integer How many cores to use
exome	boolean If TRUE, calculate mappability for exons instead of window
chr.sub	logical if TRUE replace chr prefix in seqnames, default TRUE

Author(s)

Trent Walradt

mskilab/fragCounter documentation built on Jan. 27, 2024, 2:35 p.m.