Calculates the median allelic bias

median_AB calculates median allelic bias of a given locus, i.e. the heterozygous reference allele ratio. It does this by ordering the samples according to degree of heterozygosity (i.e. minor over major allele count), then calculating the location of the "median heterozyogous sample" assuming HWE given input parameters (allelefreq, inbr) as round(number of samples \* allelefreq \* (1 - allelefreq) \* (1 - inbr)), 2 times this unrounded number being the expected number of heterozygotes. Of this median heterozygous observation, the allelic bias is returned (reference over total allele ratio).

median_AB(ref_counts, var_counts, allelefreq, inbr = 0)

Arguments

ref_counts

Numeric vector. Reference counts.

var_counts

Numeric vector. Variant counts.

allelefreq

Number. Allele frequency.

inbr

Number. Inbreeding coefficient (default = 0).

Value

Median heterozygous allelic bias of ref_counts and var_counts taking into account allelefreq and inbr.

Examples

median_AB(c(5, 8, 10, 3, 5, 6, 23), c(8, 8, 6, 4, 4, 10, 0), 0.5, 0.12)
#> [1] 0.5555556
median_AB(c(5, 0, 0, 3, 5, 1, 23), c(1, 8, 6, 2, 0, 10, 0), 0.5, 0.12)
#> [1] 0.8333333
median_AB(c(5, 0, 0, 3, 5, 1, 23), c(1, 8, 6, 2, 0, 10, 0), 0.5)
#> [1] 0.8333333