Plink Utils¶
This module provides useful functions and scripts for efficient interactions
with PLINK’s output files. For example, the majority of PLINK’s output files are
spaced delimited, and are formated in such a way that it is “beautiful” to the
human eye, but is a bit harder to parse using a script compared to tabulated
files. The pyGenClean.PlinkUtils.createRowFromPlinkSpacedOutput()
function helps producing an array of all the fields for each line.
Comparing BIM files¶
Another example is the fact that when PLINK removes a certain amount of markers
from the data file, it just gives the number of excluded markers, but not a
list. The pyGenClean.PlinkUtils.compare_bim module creates a list of
markers that were removed from the original dataset when compared with the new
one. Here is the usage of the standalone script:
$ pyGenClean_compare_bim --help
usage: pyGenClean_compare_bim [-h] [-v] --before FILE --after FILE
[--out FILE]
Compares BIM file.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Input File:
--before FILE The name of the bim FILE before modification.
--after FILE The name of the bim FILE after modification.
Output File:
--out FILE The prefix of the output files. [default: snp_removed]
Subsetting a dataset¶
A useful standalone script is the pyGenClean.PlinkUtils.subset_data
module. It helps in subsetting a dataset by keeping or removing a set of
samples, and at the same time extracting or excluding a set of markers. The
following standalone script is available for the user:
$ pyGenClean_subset_data --help
usage: pyGenClean_subset_data [-h] [-v] --ifile FILE [--is-bfile] [--is-tfile]
[--is-file] [--exclude FILE] [--extract FILE]
[--remove FILE] [--keep FILE] [--out FILE]
Subsets genotype data using Plink.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Input File:
--ifile FILE The input file prefix. The format will be specified by --is-
bfile, --is-tfile or --is-file, for bfile, tfile and file,
respectively.
--is-bfile The file specified by --ifile is a bfile
--is-tfile The file specified by --ifile is a tfile
--is-file The file specified by --ifile is a file
Options:
--exclude FILE A file containing SNPs to exclude from the data set.
--extract FILE A file containing SNPs to extract from the data set.
--remove FILE A file containing samples (FID and IID) to remove from the
data set.
--keep FILE A file containing samples (FID and IID) to keep from the
data set.
Output File:
--out FILE The prefix of the output files. [default: subset]
The standalone script works with the three most used PLINK’s format: pedfile,
transposed and binary pedfiles. The --is-bfile, --is-tfile and
--is-file options tell the standalone script what is the format of the input
file. The output file format will be the same as the input one.
The Algorithm¶
For more information about the actual algorithms and source codes, refer to the following pages.