GC.fun: GC content calculator

In mskilab/fragCounter: GC mappability correction and segmentation

GC content calculator

Description

Calculates GC content across the genome for a given sized window

Usage

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

Arguments

win.size	integer Window size, in basepairs, to calculate GC content for (should match window size of your coverage file
twobitURL	string URL to twobit genome file. Default is hg19 from UCSC
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	boolean 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.