roadmap/docs/02.genomic_regions_utilities.md

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

Utilities for analyzing genomic regions

There are several functions in the epik package which provides convinient ways to analyze genomic regions. This document demostrates the usage of these functions.

First we configure how to read data:

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

Basic statistics

basic_genomic_regions_stat() simply makes barplots for some basic statistics for genomic regions. There are following statistics:

• proportion: proportion in genome. If by_chr = TRUE, each bar represents the proportion in each chromosome.
• number: number of regions. If by_chr = TRUE, each bar represents the number of regions in each chromosome.
• median_width: meidan width of regions. If by_chr = TRUE, each bar represents the meidan width in each chromosome.

We use H3K4me1 peaks as an example:

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