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

CCFold

R Documentation

CCFold

Description

Bins, loess smooths and calculates folds of yeast or human CC-seq data quickly using data.table.

Usage

CCFold(
  in.mode = "fullmap",
  s.dir = getwd(),
  c.dir,
  exp.name,
  genome = "Cer3H4L2",
  bin.width = 100,
  sc = 80,
  si = 100,
  os = 0,
  mcal = F,
  rDNAcal = F,
  cal.path,
  out.mode1 = "full",
  out.mode2 = "strand",
  plot.mode = T,
  ylims = "auto",
  gene.track = F,
  ARS.track = T,
  names
)

Arguments

`in.mode`	Reading in .RDS file or a folder of FullMaps? Choose "rds" or "fullmap". Defaults to "rds".
`s.dir`	A character string defining the RDS file or folder containing the SAMPLE FullMaps.
`c.dir`	A character string defining the RDS file or folder containing the CONTROL 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.
`sc`	Parameter which changes the "span" of the smooth. Higher numbers will give a broader smooth.
`si`	Parameter which alters the final number of points of the smooth curve to be plotted. Defaults to 100 bp.
`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.
`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? (T/F). Defaults to TRUE.
`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.
`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.
`names`	Can specify your own vector of alias names for the libraries.