Goodness-of-fit test for symmetry.

symmetry_gof calculates the chi-squared test for symmetry of allelic counts. This tests whether the number of samples expressing more than 50 correspond to the amounts we expect when assuming HWE AS WELL AS no allelic shift (on average equal expression of reference- and variant alleles in heterozygotes). These are the expected number of homozygote ref-samples plus half the expected number of heterozygous samples, and the expected number of homozygote var-samples plus half the expected number of heterozygous samples, both under HWE, respectively. This function is used during imprinting analyses ONLY, as these are the assumptions made during those analyses.

symmetry_gof(ref_counts, var_counts, allelefreq)

Arguments

ref_counts

Numeric list. Reference counts.

var_counts

Numeric list. Variant counts.

allelefreq

Number. Allele frequency.

Value

The p-value of chi-squared test for ref_counts and var_counts.

Examples

symmetry_gof(c(5, 8, 10, 3, 5, 6, 23, 4, 12, 10, 9, 6, 7, 25),
c(8, 8, 6, 4, 4, 10, 0, 7, 8, 4, 2, 7, 15, 13), 0.5)
#> [1] 1
symmetry_gof(c(5, 0, 0, 3, 5, 1, 23, 0, 12, 0, 9, 0, 1, 0),
c(1, 8, 6, 2, 0, 10, 0, 7, 0, 4, 0, 7, 0, 13), 0.5)
#> [1] 1