Augment the loci table with information from a analysis object
Source:R/augment_loci.R
augment_loci.Rdaugment_loci add columns to the loci table of a gen_tibble related to
information from a given analysis.
Arguments
- x
An object returned by one of the
gt_functions (e.g.gt_pca()).- data
the
gen_tibbleused to run the PCA.- ...
Additional parameters passed to the individual methods.
Value
A loci tibble with additional columns. If data is missing, a tibble
of the information, with a column .rownames giving the loci names.
Examples
# Create a gen_tibble of lobster genotypes
bed_file <-
system.file("extdata", "lobster", "lobster.bed", package = "tidypopgen")
lobsters <- gen_tibble(bed_file,
backingfile = tempfile("lobsters"),
quiet = TRUE
)
# Remove monomorphic loci and impute
lobsters <- lobsters %>% select_loci_if(loci_maf(genotypes) > 0)
lobsters <- gt_impute_simple(lobsters, method = "mode")
# Create PCA
pca <- gt_pca_partialSVD(lobsters)
# Augment the gen_tibble with the PCA scores
augment_loci(pca, data = lobsters)
#> # A tibble: 79 × 17
#> big_index name chromosome position genetic_dist allele_ref allele_alt
#> <int> <chr> <fct> <int> <dbl> <chr> <chr>
#> 1 1 rs3441 1 1 1 G A
#> 2 2 rs4173 2 2 2 C T
#> 3 3 rs6157 3 3 3 G C
#> 4 4 rs7502 4 4 4 C T
#> 5 5 rs7892 5 5 5 A T
#> 6 6 rs9441 7 7 7 A G
#> 7 7 rs11071 8 8 8 G A
#> 8 8 rs11183 9 9 9 A G
#> 9 9 rs11291 10 10 10 T G
#> 10 10 rs12971 11 11 11 A G
#> # ℹ 69 more rows
#> # ℹ 10 more variables: .loadingPC1 <dbl>, .loadingPC2 <dbl>, .loadingPC3 <dbl>,
#> # .loadingPC4 <dbl>, .loadingPC5 <dbl>, .loadingPC6 <dbl>, .loadingPC7 <dbl>,
#> # .loadingPC8 <dbl>, .loadingPC9 <dbl>, .loadingPC10 <dbl>