write.apply.polygenic.score.output.to.file

A utility function that writes the two data frames outputted by apply.polygenic.score to two tab-delimited text files.

Simple and transparent parsing of genotype/dosage data
from an input Variant Call Format (VCF) file, matching of genotype
coordinates to the component Single Nucleotide Polymorphisms (SNPs)
of an existing polygenic score (PGS), and application of SNP weights
to dosages for the calculation of a polygenic score for each individual
in accordance with the additive weighted sum of dosages model. Methods
are designed in reference to best practices described by
Collister, Liu, and Clifton (2022) <doi:10.3389/fgene.2022.818574>.

Paul Boutros

ApplyPolygenicScore

Utilities for the Application of a Polygenic Score to a VCF

Nicole Zeltser

Rachel Dang

Raag Agrawal

write.apply.polygenic.score.output.to.file function

<dl><dt>apply.polygenic.score.output</dt>
<dd>list of two data frames: <code>pgs.output</code> and <code>regression.output</code></dd>
<dt>output.dir</dt>
<dd>character string of the path to write both output files</dd>
<dt>file.prefix</dt>
<dd>character string of the file prefix to use for both output files</dd></dl>

Arguments

Write apply.polygenic.score output to file — write.apply.polygenic.score.output.to.file

<dl>

<dt>apply.polygenic.score.output</dt>
<dd>list of two data frames: <code>pgs.output</code> and <code>regression.output</code></dd>


<dt>output.dir</dt>
<dd>character string of the path to write both output files</dd>


<dt>file.prefix</dt>
<dd>character string of the file prefix to use for both output files</dd>

</dl>

write.apply.polygenic.score.output.to.file: Write apply.polygenic.score output to file

Description

Usage

Arguments