enrich_with_histone_mark: Normalize histone modification signals to target regions

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

Description

Normalize histone modification signals to target regions

Usage

enrich_with_histone_mark(target, mark, sample_id, mode = mean, return_arr = FALSE, ...)

Arguments

target	target regions
mark	name of the histone mark
sample_id	a vector of sample IDs
mode	how to summarize histone modification signals among samples, by defualt is the cross-sample mean signal
return_arr	whether also return the three dimension array itself
...	pass to normalizeToMatrix

Details

For each sample, the signal is normalized as a matrix, which results an array in which the third dimension corresponds to samples. The final normalized matrix which shows e.g. mean signal matrix is calcualted by apply(array, c(1, 2), mode).

Value

If return_arr is set to FALSE, the funtion returns a matrix which can be directly sent to EnrichedHeatmap. If return_arr is TRUE, the returned value is a list in which the first element is the original array and the second element is the normalized matrix.

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.