heatmap_diff_methylation_in_genomic_features: Heatmap for differential methylated genomic features

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

Description

Heatmap for differential methylated genomic features

Usage

heatmap_diff_methylation_in_genomic_features(gr, subgroup,
    ha = HeatmapAnnotation(subgroup = subgroup, show_annotation_name = TRUE),
    genomic_features = NULL,
    meth_diff = 0, cutoff = 0.05, adj_method = "BH",
    cluster_columns = c("subgroup", "all", "none"), ...)

Arguments

gr	a GRanges object returned from get_mean_methylation_in_genomic_features
subgroup	subgroup information
ha	column annotations, a HeatmapAnnotation-class object
genomic_features	a single or a list of GRanges objects that are used to annotate gr
meth_diff	minimal range between mean value in subgroups
cutoff	if subgroup information is provided, cutoff of p-value of the oneway ANOVA test
adj_method	method to calculate adjusted p-values
cluster_columns	how to cluster columns. "subgroup" means only to cluster samples in every subgroup.
...	pass to Heatmap

Details

Only those regions having differential methylation are visualized.

Value

A GRanges object which only contains regions with significant differential methylation.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

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