methylation_qcplot: Basic qc plot for distribution of methylation and CpG...

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

Description

Basic qc plot for distribution of methylation and CpG coverage

Usage

methylation_qcplot(sample_id, chromosome = paste0("chr", 1:22), background = NULL)

Arguments

sample_id	a vector of sample IDs. You can generate plots for a list of samples in a batch which is faster than making it one by one.
chromosome	a vector of chromosome names
background	background regions where the CpG sites will only be looked into

Details

For each sample id, it will produce five plots:

• mean/median CpG coverage per chromosome, red area corresponds to the 25th and 75th percential.

• histogram of CpG coverage

• mean/median methylation per chromosome, red area corresponds to the 25th and 75th percential.

• histogram of methylation

• mean/median Methylation at each CpG coverage , red area corresponds to the 25th and 75th percential at each CpG coverage.

Value

A list of corresponding statistics

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

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