michailidou

A data.table containing a subset of <a href="https://www.nature.com/articles/nature24284/">Michailidou et al., 2017</a> breast cancer summary statistic dataset, in hg38 build.
This dataset is freely available in GWAS catalog (see link below). I removed unnecessary and all-missing columns, and rows
with missing data at hm_beta and hm_effect_allele_frequency, 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 LD matrix computation or parameter tuning. Reales,G., Kelemen,M., Wallace,C. (2020) <doi:10.1101/2020.07.24.220392> "R<c3><a1>pidoPGS: A rapid polygenic score calculator for summary GWAS data without validation dataset".

Guillermo Reales

RapidoPGS

A Fast and Light Package to Compute Polygenic Risk Scores

Chris Wallace

Olly Burren

michailidou function

A data.table object containing 100,000 SNPs<dl class="dl-horizontal">
<dt>hm_rsid</dt><dd>rsids, or SNP ids</dd>
<dt>hm_chrom</dt><dd>chromosome</dd>
<dt>hm_pos</dt><dd>base position, in hg38</dd>
<dt>hm_other_allele</dt><dd>reference, or non-effect allele</dd>
<dt>hm_effect_allele</dt><dd>alternative, or effect allele</dd>
<dt>hm_beta</dt><dd>beta, log(OR), or effect size</dd>
<dt>hm_effect_allele_frequency</dt><dd>effect allele frequency</dd>
<dt>standard_error</dt><dd>standard error of beta</dd>
<dt>p_value</dt><dd>p-value</dd>
</dl>

Format

A data.table containing a subset of <a href='https://www.nature.com/articles/nature24284/'>Michailidou et al., 2017</a> breast cancer summary statistic dataset, in hg38 build.
This dataset is freely available in GWAS catalog (see link below). I removed unnecessary and all-missing columns, and rows
with missing data at hm_beta and hm_effect_allele_frequency, and took a random sample of 100,000 SNPs without replacement.

Subset of Michailidou BRCA GWAS sumstat dataset. — michailidou

A data.table object containing 100,000 SNPs<dl class='dl-horizontal'>
<dt>hm_rsid</dt><dd>rsids, or SNP ids</dd>
<dt>hm_chrom</dt><dd>chromosome</dd>
<dt>hm_pos</dt><dd>base position, in hg38</dd>
<dt>hm_other_allele</dt><dd>reference, or non-effect allele</dd>
<dt>hm_effect_allele</dt><dd>alternative, or effect allele</dd>
<dt>hm_beta</dt><dd>beta, log(OR), or effect size</dd>
<dt>hm_effect_allele_frequency</dt><dd>effect allele frequency</dd>
<dt>standard_error</dt><dd>standard error of beta</dd>
<dt>p_value</dt><dd>p-value</dd>
</dl>

michailidou: Subset of Michailidou BRCA GWAS sumstat dataset.

Description

Usage

Arguments

Format