michailidou19: Subset of Michailidou BRCA GWAS sumstat dataset.

In GRealesM/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 \Sexpr[results=rd]{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.

Usage

michailidou19

Format

A data.table object containing 100,000 SNPs

SNPID, CHR, BP, REF, ALT, ALT_FREQ, BETA, SE, P

SNPID

rsids, or SNP ids

CHR

chromosome

BP

base position, in hg38

REF

reference, or non-effect allele

ALT

alternative, or effect allele

ALT_FREQ

effect allele frequency

BETA

beta, log(OR), or effect size

SE

standard error of beta

P

p-value

Source

http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST004001-GCST005000/GCST004988/harmonised/29059683-GCST004988-EFO_0000305-build37.f.tsv.gz

GRealesM/RapidoPGS documentation built on Feb. 20, 2025, 12:35 p.m.