michailidou38: Subset of Michailidou BRCA GWAS sumstat dataset.

In RapidoPGS: A Fast and Light Package to Compute Polygenic Risk Scores

Subset of Michailidou BRCA GWAS sumstat dataset.

Description

A data.table containing a subset of Michailidou et al., 2017 breast cancer summary statistic dataset, in hg38 build. This dataset is freely available in GWAS catalog (see link below). We 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.

Usage

michailidou38

Format

A data.table object containing 100,000 SNPs

hm_rsid

rsids, or SNP ids

hm_chrom

chromosome

hm_pos

base position, in hg38

hm_other_allele

reference, or non-effect allele

hm_effect_allele

alternative, or effect allele

hm_beta

beta, log(OR), or effect size

hm_effect_allele_frequency

effect allele frequency

standard_error

standard error of beta

p_value

p-value

Source

http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST004001-GCST005000/GCST004988/harmonised/29059683-GCST004988-EFO_0000305.h.tsv.gz

RapidoPGS documentation built on Oct. 13, 2023, 5:11 p.m.