Calculate median imprinting.

median_imprinting calculates median imprinting of allelic counts for a locus. 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 degree of imprining is returned as 2 \* (0.5 - minor over major allele count).

median_imprinting(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 degree of imprinting of ref_counts and var_counts taking into account allelefreq and inbr.

Examples

median_imprinting(c(5, 8, 10, 3, 5, 6, 23), c(8, 8, 6, 4, 4, 10, 0), 0.5, 0.12)
#> [1] -0.6
median_imprinting(c(5, 0, 0, 3, 5, 1, 23), c(1, 8, 6, 2, 0, 10, 0), 0.5, 0.12)
#> [1] 0.6
median_imprinting(c(5, 0, 0, 3, 5, 1, 23), c(1, 8, 6, 2, 0, 10, 0), 0.5)
#> [1] 0.6