get_mean_methylation_in_genomic_features: Calculate mean methylation in a list of genomic features

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Calculate mean methylation in a list of genomic features

Usage

get_mean_methylation_in_genomic_features(sample_id, genomic_features, chromosome = paste0("chr", 1:22))

Arguments

sample_id	a vector of sample IDs
genomic_features	a list or a single GRanges objects
chromosome	a vector of chromosome names

Value

A list of or a single GRanges objects (according to genomic_features you specified) in which mean methylation matrix and number of CpG in each region are attached. The variable can be sent to heatmap_diff_methylation_in_genomic_features to visualize.

Note it should be kept in mind that it doesn't make any sense to calculate mean methylation in long regions where there are hetergenuous methylation patterns.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.