23. dmc_fisher.py

23.1. Description

This program performs differential CpG analysis using Fisher exact test on proportion value. It applies to two sample comparison with no biological/technical replicates. If biological/ technical replicates are provided, methyl reads and total reads of all replicates will be merged (i.e. ignores biological/technical variations)

23.2. Input file format

# number before "," indicates number of methyl reads, and number after "," indicates
# number of total reads
cgID        sample_1    sample_2
CpG_1       129,170     166,178
CpG_2       24,77       67,99

23.3. 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) or accessible url.
 Group file defining the biological groups of each sample. It is a comma-separated 2 columns file with the 1st column containing sample IDs, and the 2nd column containing group IDs. It must have a header row. Sample IDs should match to the “Data file”.
-o OUT_FILE, --output=OUT_FILE
 The prefix of the output file.

23.4. Input files (examples)

23.5. Commands

$ dmc_fisher.py -i test_09.tsv.gz -g test_09.grp.csv -o test_fisher

23.6. Output

  • 3 columns (“Odds ratio”, “pvalue” and “FDR adjusted pvalue”) will append to the original table.
$ head -5 test_fisher.pval.txt
ID     LTS_MCR-1008    LTS_MCR-1035    STS_MCR-1021    STS_MCR-1251    OddsRatio       pval    adj.pval
chr10:100011340        12,14   26,37   0,18    10,24   9.353846153846154       1.2116597355208375e-06  6.343768248800197e-05
chr10:100011341        0,21    0,54    0,26    0,19    nan     1.0     1.0
chr10:100011387        0,14    0,40    0,20    0,24    nan     1.0     1.0
chr10:100011388        18,18   47,54   19,23   18,19   1.2548262548262548      0.7574366471769988      1.0
chr10:100026933        16,30   28,55   7,40    13,19   2.0926829268292684      0.04119183894184185     0.2617016451197068