heatmap_diff_methylation_in_genomic_features: Heatmap for differential methylation in genomic features

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

Description

Heatmap for differential methylation in genomic features

Usage

heatmap_diff_methylation_in_genomic_features(gr, annotation,
    annotation_color = structure(seq_along(unique(annotation)), names = unique(annotation)),
    txdb = NULL, gf_list = NULL, gf_type = "percent",
    min_mean_range = 0.2, cutoff = 0.05, adj_method = "BH", title = NULL,
    cluster_cols = c("subgroup", "all", "none"), ha = NULL, ...)

Arguments

gr	a GRanges object returned by get_mean_methylation_in_genomic_features
annotation	classification of samples
annotation_color	colors of classifications
txdb	A TxDb object
gf_list	a list of genomic features in GRanges which are used as row annotations
gf_type	how to overlap genomic features, pass to annotate_to_genomic_features
min_mean_range	minimal range between mean value in classifications
cutoff	if classification information is provided, p-value for the oneway ANOVA test
adj_method	how to calculate adjusted p-values
title	title of the plot
cluster_cols	how to cluster columns
ha	column annotations added to the heatmap
...	pass to Heatmap

Details

Regions have differential methylation are only visualized.

Value

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

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.