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

Utilities for analyzing methylation data

library(GlobalOptions)
library(GenomicRanges)
source("~/project/development/epik/R/read_data_hooks.R")
library(GenomicFeatures)
source("~/project/development/epik/R/genomic_region_annotation.R")
source("~/project/development/epik/R/methylation_genomic_features.R")
source("~/project/development/epik/R/methylation_qc_and_distribution.R")
library(circlize)
library(ComplexHeatmap)
library(EnrichedHeatmap)
library(gtrellis)
library(GetoptLong)

library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    warning = FALSE)

First we configure how to read data:

source("~/project/development/epik/roadmap/data_config.R")

wgbs_qcplot(SAMPLE_ID[1])
wgbs_qcplot(SAMPLE_ID[1], background = CGI)
wgbs_qcplot(SAMPLE_ID[1], background = CGI_SHORE)

gtrellis_coverage_and_methylation(SAMPLE_ID[1], nrow = 3, compact = TRUE)

gtrellis_methylation_for_multiple_samples(SAMPLE_ID, subgroup = SUBGROUP, nrow = 3, compact = TRUE)

ha = HeatmapAnnotation(subgroup = SUBGROUP, col = list(subgroup = SUBGROUP_COLOR))
global_methylation_distribution(SAMPLE_ID, subgroup = SUBGROUP, ha = ha)
global_methylation_distribution(SAMPLE_ID, subgroup = SUBGROUP, ha = ha, 
    background = CGI, meth_range = c(0, 0.1))
global_methylation_distribution(SAMPLE_ID, subgroup = SUBGROUP, ha = ha, 
    background = CGI_SHORE)

sid = SAMPLE_ID[1]
peak_list = lapply(MARKS, function(mk) chipseq_hooks$peak(mk, sid))
names(peak_list) = MARKS
gf_list = list(gene = GENE, promoter = PROMOTER, cgi = CGI, cgi_shore = CGI_SHORE)
gr = get_mean_methylation_in_genomic_features(SAMPLE_ID, peak_list)
gr[[1]]
heatmap_diff_methylation_in_genomic_features(gr[[1]], subgroup = SUBGROUP, ha = ha,
    min_mean_range = 0.2, cutoff = 0.01, genomic_features = gf_list)

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