subset_methrix: Subsets 'methrix' object based on given conditions.

View source: R/methrix_operations.R

subset_methrixR Documentation

Subsets methrix object based on given conditions.

Description

Subsets methrix object based on given conditions.

Usage

subset_methrix(
  m,
  regions = NULL,
  contigs = NULL,
  samples = NULL,
  overlap_type = "within"
)

Arguments

m

methrix object

regions

genomic regions to subset by. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object

contigs

chromosome names to subset by

samples

sample names to subset by

overlap_type

defines the type of the overlap of the CpG sites with the target region. Default value is 'within'. For detailed description, see the foverlaps function of the data.table package.

Details

Takes methrix object and filters CpGs based on coverage statistics

Value

An object of class methrix

Examples

data('methrix_data')
#Subset to chromosome 1
subset_methrix(methrix_data, contigs = 'chr21')

CompEpigen/methrix documentation built on July 24, 2024, 5:49 p.m.