Show the genotypes of a gen_tibble

Extract the genotypes (as a matrix) from a gen_tibble.

Usage

show_genotypes(.x, indiv_indices = NULL, loci_indices = NULL, ...)

# S3 method for class 'tbl_df'
show_genotypes(.x, indiv_indices = NULL, loci_indices = NULL, ...)

# S3 method for class 'vctrs_bigSNP'
show_genotypes(.x, indiv_indices = NULL, loci_indices = NULL, ...)

Arguments

.x

a vector of class vctrs_bigSNP (usually the genotype column of a gen_tibble object), or a gen_tibble.

indiv_indices

indices of individuals

loci_indices

indices of loci

...

currently unused.

Value

a matrix of counts of the alternative alleles (see show_loci()) to extract information on the alleles for those loci from a gen_tibble.

Examples

example_gt <- load_example_gt("gen_tbl")

example_gt %>% show_genotypes()
#>      [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,]    1    1    0    1    1    0
#> [2,]    2    1    0   NA    0    0
#> [3,]    2   NA    0    0    1    1
#> [4,]    1    0    0    1    0    0
#> [5,]    1    2    0    1    2    1
#> [6,]    0    0    0    0   NA    1
#> [7,]    0    1    1    0    1   NA