Munge GWAS summary statistics

munge() applies 5 filters (if possible):

1. Deduplication of RSID

2. Filter variants on INFO in INFO column is present

3. Filter variant on effect allele frequency

4. Removes strand ambigious variants

5. Removes variants with N < round(stats::quantile(N, 0.9) / 1.5)

Usage

munge(dset, info_filter = 0.9, eaf_filter = 0.01)

Arguments

dset

a dplyr::tibble() with columns SNP, A1 A2 Z N and optional columns EAF and INFO

info_filter

INFO score filter threshold at which to remove rows

eaf_filter

effective allele filter at which to remove rows. eaf_filter=0.01 would filter to eaf > 0.01 & eaf < 0.99

Value

a data.frame

Examples

if (FALSE) { # \dontrun{
munge(tbl)
} # }