michailidou38 {RapidoPGS} | R Documentation |
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
[Package RapidoPGS version 2.3.0 Index]