13. beta_m_conversion.py

13.1. Description

Convert Beta-value into M-value or vice vers

Example of input (beta)

CpG_ID Sample_01 Sample_02 Sample_03 Sample_04 cg_001 0.831035 0.878022 0.794427 0.880911 cg_002 0.249544 0.209949 0.234294 0.236680 cg_003 0.845065 0.843957 0.840184 0.824286

13.2. Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

-i INPUT_FILE, --input_file=INPUT_FILE

Tab-separated data frame file containing beta values with the 1st row containing sample IDs and the 1st column containing CpG IDs. This file can be a regular text file or compressed file (.gz, .bz2).

-d DATA_TYPE, --dtype=DATA_TYPE

Input data type either “Beta” or “M”.

-o OUT_FILE, --output=OUT_FILE

The output file.

13.3. Input file (example)

test_08.tsv.gz

13.4. Command

$ beta_m_conversion.py  -i test_08.tsv -d Beta -o test_08_M.tsv

13.5. Output

$ head -5 test_08_M.tsv
cg_ID  TCGA-BC-A10Q    TCGA-BC-A10R    TCGA-BC-A10S    TCGA-BC-A10T    TCGA-BC-A10U
cg00000029     -0.9127840676229807     -0.6635535075463712     -0.9389653708375745     -1.1786876012968779     -0.6217264255944122
cg00000165     -2.4833534763405667     -2.3330364850204406     -2.858145170950326      -2.914508967160336      -2.3645896606652745
cg00000236     2.478873972561897       3.0777336083377693      2.6760378499862143      3.04301970048709        2.7096166677505145
cg00000289     0.9943771370790748      0.13339998728363872     0.5981994318909333      1.2402989291699527      1.432741941887314