Plate Bias Module

The usage of the standalone module is shown below:

$ pyGenClean_plate_bias --help
usage: pyGenClean_plate_bias [-h] [-v] --bfile FILE --loop-assoc FILE
                             [--pfilter FLOAT] [--out FILE]

Checks for plate bias.

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

Input File:
  --bfile FILE       The input file prefix (will find the plink binary files
                     by appending the prefix to the .bim, .bed and .fam files,
                     respectively.
  --loop-assoc FILE  The file containing the plate organization of each
                     samples. Must contains three column (with no header):
                     famID, indID and plateName.

Options:
  --pfilter FLOAT    The significance threshold used for the plate effect.
                     [default: 1.0e-07]

Output File:
  --out FILE         The prefix of the output files. [default: plate_bias]

Input Files

This module uses PLINK’s binary file format (bed, bim and fam files) for the source data set (the data of interest).

Procedure

Here are the steps performed by the module:

  1. Runs the plate bias analysis using Plink.
  2. Extracts the list of significant markers after plate bias analysis.
  3. Computes the frequency of all significant markers after plate bias analysis.

Output Files

The output files of each of the steps described above are as follow (note that the output prefix shown is the one by default [i.e. plate_bias]):

  1. One set of PLINK’s result files:
    • plate_bias: this includes file like plate_bias.PLATE_NAME.assoc.fisher containing a list of markers that were significant after the plate bias analysis.
  2. One file:
    • plate_bias.significant_SNPs.txt: a file containing a list of markers that were significant after the plate bias analysis (contained in all the *.fisher files).
  3. One set of PLINK’s result files:
    • plate_bias.significant_SNPs: the result files containing the frequency of all the markers that were significant after the plate bias analysis (contained in all the *.fisher files).

The Algorithm

For more information about the actual algorithms and source codes, refer to the following page.