EUR_ld.blocks38

A GRanges object containing the LD block for European ancestry, in hg38 build.
This dataset was obtained from <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731402/">Belisa and Pickrell (2016)</a>, in bed format,
then liftovered to hg38 using UCSC liftOver tool, then converted to GRanges.
See manuscript for more details.

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

EUR_ld.blocks38 function

A GRanges object containing 1625 ranges<dl class="dl-horizontal">
<dt>seqnames</dt><dd>chromosome</dd>
<dt>ranges</dt><dd>start and stop positions for the block</dd>
<dt>strand</dt><dd>genomic strand, irrelevant here</dd>
</dl>

Format

A GRanges object containing the LD block for European ancestry, in hg38 build.
This dataset was obtained from <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731402/'>Belisa and Pickrell (2016)</a>, in bed format,
then liftovered to hg38 using UCSC liftOver tool, then converted to GRanges.
See manuscript for more details.

LD block architecture for European populations (hg38). — EUR_ld.blocks38

A GRanges object containing 1625 ranges<dl class='dl-horizontal'>
<dt>seqnames</dt><dd>chromosome</dd>
<dt>ranges</dt><dd>start and stop positions for the block</dd>
<dt>strand</dt><dd>genomic strand, irrelevant here</dd>
</dl>

EUR_ld.blocks38: LD block architecture for European populations (hg38).

Description

Usage

Arguments

Format