Reads in the output from plink2 --make-king-table (documentation).
Input file must have six columns, tab delimited:
id1 (member 1)
id2 (member 2)
nsnps
hethet: proportion of sites where both are heterozygous
k: Kinship Coefficient
read_plink2_king(file)Input file path
A tibble containing the 6 columns from the plink2 --make-king-table output.
plink2kingFile <- system.file("extdata", "plink2-king-table.tsv", package="skater", mustWork=TRUE)
plink2king <- read_plink2_king(plink2kingFile)
plink2king
#> # A tibble: 45 × 6
#> id1 id2 nsnps hethet ibd0 k
#> <chr> <chr> <int> <dbl> <dbl> <dbl>
#> 1 g1-b1-i1 g1-b1-s1 590330 0.0639 0.0326 -0.0115
#> 2 g1-b1-s1 g2-b1-s1 590330 0.0649 0.0324 -0.00387
#> 3 g1-b1-i1 g2-b1-s1 590330 0.0628 0.0332 -0.0140
#> 4 g1-b1-s1 g2-b1-s2 590330 0.0649 0.0325 -0.000565
#> 5 g1-b1-i1 g2-b1-s2 590330 0.0631 0.0334 -0.0182
#> 6 g2-b1-s1 g2-b1-s2 590330 0.0643 0.0329 -0.00832
#> 7 g1-b1-s1 g2-b1-i1 590330 0.0899 0 0.247
#> 8 g1-b1-i1 g2-b1-i1 590330 0.0875 0 0.244
#> 9 g2-b1-i1 g2-b1-s1 590330 0.0640 0.0321 -0.000468
#> 10 g2-b1-i1 g2-b1-s2 590330 0.0641 0.0325 -0.00622
#> # … with 35 more rows
plink2king %>% dplyr::filter(k>0.01)
#> # A tibble: 20 × 6
#> id1 id2 nsnps hethet ibd0 k
#> <chr> <chr> <int> <dbl> <dbl> <dbl>
#> 1 g1-b1-s1 g2-b1-i1 590330 0.0899 0 0.247
#> 2 g1-b1-i1 g2-b1-i1 590330 0.0875 0 0.244
#> 3 g1-b1-s1 g2-b1-i2 590330 0.0898 0 0.246
#> 4 g1-b1-i1 g2-b1-i2 590330 0.0892 0 0.248
#> 5 g2-b1-i1 g2-b1-i2 590330 0.105 0.00864 0.244
#> 6 g1-b1-s1 g2-b2-i1 590330 0.0922 0 0.253
#> 7 g1-b1-i1 g2-b2-i1 590330 0.0888 0 0.245
#> 8 g2-b1-i1 g2-b2-i1 590330 0.103 0.00926 0.233
#> 9 g2-b1-i2 g2-b2-i1 590330 0.110 0.00571 0.272
#> 10 g1-b1-s1 g2-b2-i2 590330 0.0928 0 0.254
#> 11 g1-b1-i1 g2-b2-i2 590330 0.0876 0 0.242
#> 12 g2-b1-i1 g2-b2-i2 590330 0.105 0.00957 0.239
#> 13 g2-b1-i2 g2-b2-i2 590330 0.104 0.0102 0.231
#> 14 g2-b2-i1 g2-b2-i2 590330 0.106 0.00807 0.248
#> 15 g1-b1-s1 g2-b3-i1 590330 0.0903 0 0.248
#> 16 g1-b1-i1 g2-b3-i1 590330 0.0879 0 0.245
#> 17 g2-b1-i1 g2-b3-i1 590330 0.113 0.00857 0.268
#> 18 g2-b1-i2 g2-b3-i1 590330 0.107 0.00835 0.252
#> 19 g2-b2-i1 g2-b3-i1 590330 0.0991 0.00978 0.219
#> 20 g2-b2-i2 g2-b3-i1 590330 0.0998 0.0113 0.214