mergeLoci: Combines overlaps in ys and xs
In CMWbio/geaR: GDS Evolutionary Analysis in R

mergeLoci

R Documentation

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.