Estimate individual observed heterozygosity

Estimate observed heterozygosity (H_obs) for each individual (i.e. the frequency of loci that are heterozygous in an individual).

Usage

indiv_het_obs(.x, as_counts = FALSE, ...)

# S3 method for class 'tbl_df'
indiv_het_obs(.x, as_counts = FALSE, ...)

# S3 method for class 'vctrs_bigSNP'
indiv_het_obs(.x, as_counts = FALSE, ...)

Arguments

.x

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

as_counts

logical, if TRUE, return a matrix with two columns: the number of heterozygotes and the number of missing values for each individual. These quantities can be useful to compute more complex quantities.

...

currently unused.

Value

either:

• a vector of heterozygosities, one per individuals in the gen_tibble

• a matrix with two columns, where the first is the number of heterozygous loci for each individual and the second is the number of missing values for each individual

Examples

example_gt <- load_example_gt("gen_tbl")

example_gt %>% indiv_het_obs()
#> [1] 0.6666667 0.2000000 0.4000000 0.3333333 0.5000000 0.2000000 0.6000000

# For observed heterozygosity as counts:
example_gt %>% indiv_het_obs(as_counts = TRUE)
#>      het_n na_n
#> [1,]     4    0
#> [2,]     1    1
#> [3,]     2    1
#> [4,]     2    0
#> [5,]     3    0
#> [6,]     1    1
#> [7,]     3    1