18. dmc_bb.py

18.1. Description

This program performs differential CpG analysis using “beta binomial” model on proportion values. It allows for covariant analysis.

Notes - You must install R package aod before running this program.

18.2. Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

-i INPUT_FILE, --input-file-INPUT_FILE

Data file containing methylation proportions (represented by “methyl_count,total_count”, eg. “20,30”) with the 1st row containing sample IDs (must be unique) and the 1st column containing CpG positions or probe IDs (must be unique). This file can be a regular text file or compressed file (.gz, .bz2).

-g GROUP_FILE, --group-GROUP_FILE

Group file defining the biological groups of each sample as well as other covariables such as gender, age. The first varialbe is grouping variable (must be categorical), all the other variables are considered as covariates (can be categorial or continuous). Sample IDs shoud match to the “Data file”..

-o OUT_FILE, --output-OUT_FILE

Prefix of the output file.

18.4. Command

$ python3 ../bin/dmc_bb.py -i test_04_TwoGroup.tsv.gz -g test_04_TwoGroup.grp.csv -o OUT_bb