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

Visualize global difference by Hilbert curve

library(GlobalOptions)
library(GenomicRanges)
library(memoise)
source("~/project/development/epik/R/read_data_hooks.R")
library(GenomicFeatures)
source("~/project/development/epik/R/hilbert_curve_difference.R")
source("~/project/development/epik/R/methylation_genomic_features.R")
source("~/project/development/epik/R/genomic_region_correlation.R")
source("~/project/development/epik/R/common_utils.R")
library(circlize)
library(ComplexHeatmap)
library(EnrichedHeatmap)
library(GetoptLong)
library(HilbertCurve)

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")

gr_meth = hilbert_curve_methylation_difference(subgroup = SUBGROUP,
    comparison = c("group1", "group2"), type = c("global_mean", "subgroup_mean", "difference"))
gr_meth

gr_list = lapply(MARKS, function(mk) hilbert_curve_chipseq_difference(mk, subgroup = SUBGROUP, 
    comparison = c("group1", "group2"), type = "rel_difference"))
gr_list[[1]]

names(gr_list) = MARKS
gr_meth$diff = gr_meth$mean_group1 - gr_meth$mean_group2
gr_list = lapply(gr_list, function(gr) {
    gr$diff = gr$mean_group1 - gr$mean_group2
    gr
})
general_chipseq_association_to_methylation(gr_list, gr_meth)

```r
general_chipseq_association(gr_list)
general_chipseq_association(gr_list, q = seq(0.1, 0.9, by = 0.1))

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