mergeLoci: Combines overlaps in ys and xs

In CMWbio/geaR: GDS Evolutionary Analysis in R

Combines overlaps in ys and xs

Description

Combines multiple GRangeList objects with overlapping ranges.

Usage

mergeLoci(x, y, nCores, overlap = "+", table = NULL)

Arguments

x	GRangesList. xs to overlap ys to.
y	GRangesList or character containing ys. Provide wither a GRangesList or path to SQL database.
nCores	numeric number of cores to run in parallel
overlap	character Negative or positive overlap "-" will subtract the y ranges from the xs "+" will bin ys into x ranges
table	character one of c("4Degen", "0Degen", "2Degen")

Details

Authour: Chris Ward Passing multiple GRange objects will result in ordered overlaping of ranges. e.g. if a genome wide 100kb tiled x GRangeList generated using xMaker() is passed along with a ys GRangesList generated using getwindows(y = "gene:cds"), This will be combined into 100kb xs containing only regions of protein coding sequence.

Value

A GRangesList containing merged ranges

CMWbio/geaR documentation built on July 5, 2024, 5:29 p.m.