michailidou19

A data.table containing a subset of tools:::Rd_expr_doi("10.1038/nature24284") breast cancer summary statistic dataset, in hg19 build.
This dataset is freely available in GWAS catalog (see link below). We used "chromosome", "base_pair_location columns", removed unnecessary and all-missing columns, and took a random sample of 100,000 SNPs without replacement.

datasets

Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".

Guillermo Reales

RapidoPGS

A Fast and Light Package to Compute Polygenic Risk Scores

Chris Wallace

Olly Burren

michailidou19 function

A data.table object containing 100,000 SNPs<dl>
SNPID, CHR, BP, REF, ALT, ALT_FREQ, BETA, SE, P
<dt>SNPID</dt>
<dd>rsids, or SNP ids</dd><dt>CHR</dt>
<dd>chromosome</dd><dt>BP</dt>
<dd>base position, in hg38</dd><dt>REF</dt>
<dd>reference, or non-effect allele</dd><dt>ALT</dt>
<dd>alternative, or effect allele</dd><dt>ALT_FREQ</dt>
<dd>effect allele frequency</dd><dt>BETA</dt>
<dd>beta, log(OR), or effect size</dd><dt>SE</dt>
<dd>standard error of beta</dd><dt>P</dt>
<dd>p-value</dd>
</dl>

Format

Subset of Michailidou BRCA GWAS sumstat dataset. — michailidou19

A data.table object containing 100,000 SNPs<dl>
SNPID, CHR, BP, REF, ALT, ALT_FREQ, BETA, SE, P
<dt>SNPID</dt>
<dd>rsids, or SNP ids</dd>

<dt>CHR</dt>
<dd>chromosome</dd>

<dt>BP</dt>
<dd>base position, in hg38</dd>

<dt>REF</dt>
<dd>reference, or non-effect allele</dd>

<dt>ALT</dt>
<dd>alternative, or effect allele</dd>

<dt>ALT_FREQ</dt>
<dd>effect allele frequency</dd>

<dt>BETA</dt>
<dd>beta, log(OR), or effect size</dd>

<dt>SE</dt>
<dd>standard error of beta</dd>

<dt>P</dt>
<dd>p-value</dd>


</dl>

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michailidou19: Subset of Michailidou BRCA GWAS sumstat dataset.

Description

Usage

Arguments

Format