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

CCBin

R Documentation

CCBin

Description

Bins yeast or human CC-seq data quickly using data.table. The outpout can be strand separated, or totalled, and can be in sparse or full format.

Usage

CCBin(
  in.mode = "fullmap",
  path.name = getwd(),
  exp.name,
  genome = "Cer3H4L2",
  bin.width = 100,
  os = 0,
  mcal = F,
  rDNAcal = F,
  cal.path,
  out.mode1 = "full",
  out.mode2 = "strand",
  plot.mode = "png",
  violin = T,
  ylims = "auto",
  ARS.track = T,
  cen.track = T,
  names,
  plotdimensions = "wide",
  bg = "white",
  samples,
  lin.mod = F
)

Arguments

`in.mode`	Reading in .RDS file or a folder of FullMaps? Choose "rds" or "fullmap". Defaults to "rds".
`path.name`	A character string defining the RDS file or folder containing FullMaps.
`exp.name`	Manually specify a name for the experiment.
`genome`	Which genome has the data been aligned to? "Cer3H4L2", "W303" or "hg19". Defaults to "Cer3H4L2".
`bin.width`	What size bins, in bp? Defaults to 100.
`os`	Do you want to offset the Crick strand relative to the Watson strand prior to binning? Choose 3 for Top2, or 1 for Spo11. Choose 0 for no ofsetting. Defaults to 3.
`mcal`	normalise based of the mitochondria
`rDNAcal`	normalise based of the rDNA
`out.mode1`	"sparse" or "full" format. Defaults to "full". Defaults to "full"
`out.mode2`	Do you want to sum the Watson and Crick strands ("total") or report them seperately ("strand")? Defaults to "strand".
`plot.mode`	Do you want to plot the binned chromosome maps as "pdf" of "png"? Choose "none" for no plots
`ylims`	A single number specifying the maximum limit of the y axis, for both Watson and Crick. OR "auto", to automatically define for the entire set.
`bg`	Choose the background for the plots. Can be "none" (transparent), or "white".
`gene.track`	Do you want to plot the gene track? This is pretty pointless on whole chromosome plots. Awaiting a more sensible implementation. Defaults to FALSE.