CCfoldHS.binning: CCfoldHS.binning

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

CCfoldHS.binning

Description

Bins smoothed hotspot log2(x/y) data

Usage

CCfoldHS.binning(
  files,
  i = 1,
  binwidth.v = c(10, 25, 50, 100),
  work.d = getwd(),
  si = 100,
  plotmode = T,
  ARSline = F,
  ylims = 2,
  control.col = "lightblue",
  mutant.col = "red",
  usesmooth = T
)

Arguments

files	a vector of filenames for a smoothed hotspot log2(x/y) table
i	position in the files vector
binwidth.v	A used of the binning binwidths in Kb
work.d	working directory
si	smooth interval default 100
plotmode	Whether to generate a plot
ARSline	whether to add ARS positions to the plot
control.col	What colour do you want the control
mutant.col	What colour do you want the mutant
usesmooth	Whether to use smoothed HS data or not. When TRUE plotmode is disabled

Examples

files <- list.files(pattern = "m")
packages.check("doParallel")
cl <- makeCluster(7)
registerDoParallel(cl)
packages.check("GenomicRanges",BiocM=T)
packages.check("ggplot2")
packages.check("ggpubr")
packages.check("GenomicFeatures",BiocM=T)
foreach (i = 1:length(files),.packages=c("nealeLabFunctions","GenomicRanges","ggplot2","ggpubr")) %dopar% {
 CCfoldHS.binning(files,i)
 }stopCluster(cl)

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