global_methylation_distribution: Global methylation distribution

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Global methylation distribution

Usage

global_methylation_distribution(sample_id, annotation,
    annotation_color = structure(seq_along(unique(annotation)), names = unique(annotation)),
    reorder_column = TRUE, ha = NULL, chromosome = paste0("chr", 1:22), by_chr = FALSE, max_cov = 100,
    background = NULL, p = 0.001)

Arguments

sample_id	a vector of sample ids
annotation	classification information
annotation_color	color for classifications
reorder_column	whether reorder the samples
ha	additional annotation can be specified as a HeatmapAnnotation object
chromosome	chromosomes
by_chr	whether make the plot by chromosome
max_cov	maximum coverage (used to get rid of extremely high coverage which affects visualization of CpG coverage distribution)
background	background to look into. The value can be a single GRanges object or a list of GRanges objects.
p	probability to randomly sample CpG sites

Details

It visualize distribution of methylation values and CpG coverages through heatmaps.

Value

If by_chr is set to FALSE, it returns a vector of column order.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.