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

CCTally

R Documentation

CCMap

Description

Maps CCs in a specific chromosome region, alongside various annotations.

Usage

CCTally(
  in.mode = "rds",
  path.name = getwd(),
  exp.name,
  genome = "Cer3H4L2",
  phase = "meiosis",
  samples,
  os = 3,
  mcal = F,
  cal.path,
  chrom.,
  pos,
  up.w,
  down.w,
  ylims = 50,
  region.mode = "manual",
  smooth.mode = "none",
  Fsize = 101,
  win = 50,
  norm.factor = 3,
  gene.track = T,
  MNase.track = T,
  out.mode = "png",
  plotdimensions = "wide",
  loci
)

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".
`phase`	"meiosis" or "vegetative"
`samples`	Which samples to plot, as a vector of indexes in the DSBList.
`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.
`chrom.`	Which chromosome to plot?
`pos`	Which coordinate to centre plot on, in bp?
`ylims`	A single number specifying the maximum limit of the y axis, for both Watson and Crick. OR "auto", to automatically define for each sample.
`region.mode`	Do you want to manually specify a region, or do you want to multiple maps centred on every TSS. CHoose "manual" (Default) or "TSS".
`smooth.mode`	This option controls whether to apply VariableX ("VX") or Hann window ("HW") smoothing to the broad overlay. Deafults to no smoothing.
`Fsize`	Fsize for VariableX (See the documentation for VX function). Only used if smooth.mode == "VX".
`win`	Hanning window width. Only used if smooth.mode == "HW".
`norm.factor`	This can be used to scale the height of the smoothed track (works for Hann or VariableX smoothing). Defaults to 3.
`gene.track`	Do you want to plot the gene track? Defaults to TRUE.
`out.mode`	"pdf" or "png" file format for output.
`window.w`	How wide a region to plot in bp?
`plot.dimensions`	Specify the plot size. Can be any size from the "A sizing" scale (e.g "A1"). However this is not implemented properly yet. Defaults to "wide", which is fine.