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A python script to automatically run MetaSKAT

compute_lambda.py is small script to execute a MetaSKAT analysis on different cohort.

Dependencies

The tool requires a standard Python installation (version 2 or 3) with the following packages:

  1. pandas version 0.17 or latest
  2. rpy2 version 2.7.7 or latest
  3. PyYAML version 3.11 or latest
  4. pyplink version 1.2.0 or latest

The tool has been tested on Linux only, but should also work on both Mac OSX and Windows.

Usage

Using either python or python3:

$ python run_metaskat.py --help
usage: run_metaskat.py [-h] [-v] -c YAML -g FILE [--mac INT] [-o DIR]

Automatically execute MetaSKAT on multiple cohorts (using rpy2).

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

INPUT OPTIONS:
  -c YAML, --conf YAML  The YAML file containing the information about the
                        cohorts.

SEGMENT OPTIONS:
  -g FILE, --gene-list FILE
                        The gene list (with markers) required by MetaSKAT
  --mac INT             The minimal MAC value to keep a segment [>4]

OUTPUT OPTIONS:
  -o DIR, --output DIR  The output directory [metaskat_output]