getRelativeCoordMats: Convert C position numbering from genomic to relative...

In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

Convert C position numbering from genomic to relative coordinates for a list of matrices

Description

Convert C position numbering from genomic to relative coordinates for a list of matrices

Usage

getRelativeCoordMats(
  matList,
  regionGRs,
  regionType,
  anchorCoord = 0,
  workDir = "."
)

Arguments

matList	A table of paths to methylation matrices with names that match the regionGRs object
regionGRs	A genomicRanges object of the regions relative to which the new coordinates are caclulated with a metadata column called "ID" containing names that match the methylation matrices in matList
regionType	A collective name for this list of regions (e.g TSS or amplicons). It will be used in naming the output directories.
anchorCoord	The coordinate which will be set as the 0 position for relative coordinates (default=0)
workDir	path to working directory

Value

A list of methylation matrices that have been converted from abslute genomic coordinates to relativepositions within the genomicRanges regionGRs. regionGRs on the negative strand will be flipped to be in the forward orientation.

jsemple19/methMatrix documentation built on Aug. 19, 2022, 3:57 p.m.