global_methylation_distribution: Global methylation distribution

Description Usage Arguments Details Examples

View source: R/methylation_stat.R

Description

Global methylation distribution

Usage

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global_methylation_distribution(sample_id, annotation,
    annotation_color = structure(seq_along(unique(annotation)), names = unique(annotation)),
    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

subtype information

annotation_color

color for subtypes

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 affect visualization of CpG coverage distribution)

background

background to look into

p

probability to randomly sample CpG sites

Details

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

Examples

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# There is no example
NULL

jokergoo/cotools documentation built on May 18, 2017, 6:05 a.m.