extractBoundaries {preciseTAD} | R Documentation

## Function to extract using boundaries from domain data

### Description

Function to extract using boundaries from domain data

### Usage

    extractBoundaries(domains.mat, preprocess = FALSE, CHR, resolution)

### Arguments

`domains.mat` | either a `matrix` or `data.frame` with at least 3 columns. First column is either of class "numeric" or "integer". The second and third columns are the start and end coordinates of domains, respectively. Required.
`preprocess` | logical, indicating whether or not domains exceeding 2mb in width or smaller than 2*(the specified resolution) should be filtered out (default is FALSE, all boundaries will be used). Required.
`CHR` | character, specifying which chromosome(s) to extract domain boundaries on (ex: "CHR22"). Required.
`resolution` | numeric, the Hi-C data resolution that domains were called at. Ignored if preprocess is FALSE.

### Value

A `GRanges` object

### Examples

    #Read in domain data from ARROWHEAD at 5 kb for GM12878
    data("arrowhead_gm12878_5kb")
    #Extract unique boundaries for CHRs 1-8 and 10-22
    bounds.GR <- extractBoundaries(domains.mat=arrowhead_gm12878_5kb,
                                   preprocess=FALSE,
                                   CHR=paste0("CHR",c(1:8,10:22)),
                                   resolution=5000)

[Package preciseTAD version 1.0.0 Index]