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

In CompEpigen/methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

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 Sept. 23, 2023, 7:14 p.m.