27. dmc_ttest.py

27.1. Description

Differential CpG analysis using T test for two groups comparison or ANOVA for multiple groups comparison.

27.2. 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 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). Except for the 1st row and 1st column, any non-numerical values will be considered as “missing values” and ignored. This file can be a regular text file or compressed file (.gz, .bz2).
 Group file defining the biological group 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”. Note: automatically switch to use ANOVA if more than 2 groups were defined in this file.
-p, --paired If True, performs a paired t-test (the paired sampels are matched by the order). If False, performs a standard independent 2 sample t-test. default=False
-w, --welch If True, performs Welch’s t-test which does not assume the two samples have equal variance. If False, performs a standard two-sample t-test (i.e. assuming the two samples have equal variance). default=False
-o OUT_FILE, --output=OUT_FILE
 The prefix of the output file.

27.4. Command

#Two group comparison. Compare normal livers to HCV-related cirrhosis livers
$dmc_ttest.py -i test_05_TwoGroup.tsv.gz -g test_05_TwoGroup.grp.csv -o ttest_2G

#Three group comparison. Compare normal livers, HCV-related cirrhosis livers, and liver cancers
$dmc_ttest.py -i test_06_ThreeGroup.tsv.gz -g test_06_ThreeGroup.grp.csv -o ttest_3G

27.5. Output files

  • ttest_2G.pval.txt
  • ttest_3G.pval.txt