enrich_with_methylation: Normalize methylation to target regions

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

Description

Normalize methylation to target regions

Usage

enrich_with_methylation(target, sample_id, mode = rowMeans, extend = 5000, smooth = TRUE, ...)

Arguments

target	target regions
sample_id	a vector of sample IDs
mode	how to summarize methylation among samples, by default it is the cross-sample mean methylation. Since methylation is represented as matrix, here we use row*-family functions (e.g. rowMeans, rowMedians)
extend	pass to normalizeToMatrix
smooth	pass to normalizeToMatrix
...	pass to normalizeToMatrix

Value

A matrix which can be directly visualized by EnrichedHeatmap

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.