CCfoldHS.binpileup: CCfoldHS.binpileup

In WHG1990/CCTools: A suite of tools for analysing CC-seq data.

CCfoldHS.binpileup

Description

Pilesup binned smoother log2(x/y) data generated from hotspot tables

Usage

CCfoldHS.binpileup(
  p.dir = getwd(),
  binwidth.v = c(100, 50, 25, 10),
  log2FoldMax = 2,
  centromere = T,
  EXT = ".png",
  invert.col = F,
  fixmax = F,
  log2foldoffset = 0,
  colhigh = "red",
  collow = "navy",
  usesmooth = T
)

Arguments

p.dir	parent directory containing the binData folder
binwidth.v	A used of the binning binwidths in Kb
log2FoldMax	max and min log2 values to plot
centromere	should the output be centered on the centromere
EXT	should the output be .png or .pdf
invert.col	should the colours be inverted
fixmax	should log2fold values higher than the max be fixed to the max. If set to false such values are displayed in gray.
log2foldoffset	value to offset log2fold values
colhigh	Choose positive colour
collow	Choose negative colour

Examples

setwd(paste0(getwd(),"/smoothed"));CCfoldHS.binpileup()

WHG1990/CCTools documentation built on June 16, 2024, 1:36 a.m.