lociRead: lociRead

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

lociRead

Description

Module for reading interpreting loci argument. Used by various CC functions, including CCMap (implemented), CCBin and CCPileup

Usage

lociRead(loci = loci, features = features, chrom. = chrom., pos = pos)

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.
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.

Author(s)

Will Gittens

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