coverage_filter {methrix}R Documentation

Filter matrices by coverage

Description

Filter matrices by coverage

Usage

coverage_filter(m, cov_thr = 1, min_samples = 1, group = NULL)

Arguments

m

methrix object

cov_thr

minimum coverage required to call a loci covered

min_samples

At-least these many samples should have a loci with coverage >= cov_thr

group

a column name from sample annotation that defines groups. In this case, the number of min_samples will be tested group-wise.

Details

Takes methrix object and filters CpGs based on coverage statistics

Value

An object of class methrix

Examples

data('methrix_data')
#keep only CpGs which are covered by at-least 1 read across 3 samples
coverage_filter(m = methrix_data, cov_thr = 1, min_samples = 3)

[Package methrix version 1.2.06 Index]