25. dmc_glm.py

25.1. Description

This program performs differential CpG analysis using generalized liner model. It allows for covariants analysis.

25.2. Options

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 beta values 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 variable is grouping variable (must be categorical), all the other variables are considered as covariates (can be categorical or continuous). Sample IDs should match to the “Data file”.

-o OUT_FILE, --output=OUT_FILE

The prefix of the output file.

25.3. Input files (examples)

• test_05_TwoGroup.tsv.gz

• test_05_TwoGroup.grp.csv

• test_05_TwoGroup.grp2.csv

25.4. Command

$dmc_glm.py  -i test_05_TwoGroup.tsv.gz -g test_05_TwoGroup.grp.csv -o GLM_2G

$dmc_glm.py  -i test_05_TwoGroup.tsv.gz -g test_05_TwoGroup.grp2.csv -o GLM_2G

25.5. Output files

• GLM_2G.results.txt

• GLM_2G.r

• GLM_2G.pval.txt (final results)