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 × 8
#> chrom id A2 A1 alt_freq obs_ct u_min u_max
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 chr22 chr22:10685239:C:T C T 0.0583 120 -3.21 3.07
#> 2 chr22 chr22:10761227:G:A G A 0.15 120 -3.01 2.95
#> 3 chr22 chr22:11285239:C:T C T 0.0833 120 -3.13 2.78
#> 4 chr22 chr22:11601805:G:A G A 0.0583 120 -2.54 2.87
#> 5 chr22 chr22:11791698:G:T G T 0.05 120 -2.74 3.27
#> 6 chr22 chr22:11797697:C:T C T 0.05 120 -2.84 3.45
#> 7 chr22 chr22:12044872:A:C A C 0.0417 120 -3.10 3.39
#> 8 chr22 chr22:12194389:G:A G A 0.0583 120 -3.18 3.28
#> 9 chr22 chr22:12207043:C:T C T 0.0583 120 -3.14 2.83
#> 10 chr22 chr22:12350816:G:A G A 0.0583 120 -3.38 3.44
#> # ℹ 165 more rows