Read a PLINK2 allele frequency file (.afreq or .afreq.zst)
Value
A data.frame with columns: chrom, id, A2 (REF), A1 (ALT), alt_freq, obs_ct. alt_freq is the frequency of the A1 (ALT/effect) allele.
Examples
stem <- file.path(system.file("extdata", "ld_reference", "chr22",
package = "pecotmr"), "protocol_example.LD.chr22")
readAfreq(stem)
#> # A tibble: 175 × 6
#> chrom id A2 A1 alt_freq obs_ct
#> <dbl> <chr> <chr> <chr> <dbl> <dbl>
#> 1 22 chr22:10685239:C:T C T 0.509 2000
#> 2 22 chr22:10761227:G:A G A 0.498 2000
#> 3 22 chr22:11285239:C:T C T 0.527 2000
#> 4 22 chr22:11601805:G:A G A 0.464 2000
#> 5 22 chr22:11791698:G:T G T 0.459 2000
#> 6 22 chr22:11797697:C:T C T 0.462 2000
#> 7 22 chr22:12044872:A:C A C 0.482 2000
#> 8 22 chr22:12194389:G:A G A 0.502 2000
#> 9 22 chr22:12207043:C:T C T 0.524 2000
#> 10 22 chr22:12350816:G:A G A 0.500 2000
#> # ℹ 165 more rows