get_mean_methylation_in_genomic_features: Calculate mean methylation value in a list of genomic...

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

Description

Calculate mean methylation value in a list of genomic features

Usage

get_mean_methylation_in_genomic_features(sample_id, gf_list, average = TRUE, p = 0.001,
    chromosome = paste0("chr", 1:22),
    filter_fun = function(s) length(s) >= 10 && any(diff(s) < 50))

Arguments

sample_id	a vector of sample IDs
gf_list	a list of genomic features in GRanges class
average	whether to calcualte average methylation in a interval? if not, the function will randomly sample CpG sites from the input regions.
p	if average is FALSE, the probability to randomly pick CpG sites
chromosome	a vector of chromosome names
filter_fun	filtering function on CpG sites in each intersection (e.g. exclude regions which contains too few CpGs). The object sent to this function is a vector of positions for CpGs that locate in the current region.

Value

A list of GRanges objects in which mean methylation matrix are attached. The variable can be sent to heatmap_diff_methylation_in_genomic_features to visualize.

= author 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.