mask_methrix: Masks too high or too low coverage

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

Masks too high or too low coverage

Description

Masks too high or too low coverage

Usage

mask_methrix(m, low_count = NULL, high_quantile = 0.99, n_cores = 1)

Arguments

m	methrix object
low_count	The minimal coverage allowed. Everything below, will get masked. Default = NULL, nothing gets masked.
high_quantile	The quantile limit of coverage. Quantiles are calculated for each sample and everything that belongs to a higher quantile than the defined will be masked. Default = 0.99.
n_cores	Number of parallel instances. Can only be used if methrix is in HDF5 format. Default = 1.

Details

Takes methrix object and masks sites with too high or too low coverage by putting NA for coverage and beta value. The sites will remain in the object.

Value

An object of class methrix

Examples

data('methrix_data')
mask_methrix(m = methrix_data, low_count = 5, high_quantile = 0.99 )

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