FullMap2bedGraph: FullMap2BedGraph

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

FullMap2BedGraph

Description

Converts FullMaps downloaded from GEO (SPECIFICALLY), into bedGraphs which can be uploaded as custom tracks to UCSC.

Usage

FullMap2bedGraph(
  path.name,
  scaling.factor = 1,
  out.dir = getwd(),
  chrom = 1:18,
  mode = "base"
)

Arguments

path.name	Character string defining the pathname to the fullmap file. Files must be in the format SAMPLENAME.FullMap.txt
scaling.factor	a scaling factor used to boost the values. This is useful in calibration, for example. Defaults to 1.
out.dir	A character string defining the pathname to the output directory. Defaults to current working directory.
chrom	A vector defining the chromosomes to process. Defaults to all chromosomes, including chromosome 3, 17 and 18, which may cause compatibility issues with UCSC.
mode	Can be "break" or "base", depending on whether you want to output the position of the DNA break (between bases), or the position of the base which is covalently linked to the protein.

Author(s)

Will Gittens

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