Logistic regression on the degree of heterozygosity between cases and controls

LOItest_logreg performs logistic regression on the degree of heterozygosity in cases compared to control samples. This tests whether there is a significant difference (p-value) between the fraction of heterozygous samples in cases versus controls, which (in the case of a higher fraction in cases) can indicate loss of imprinting.

LOItest_logreg(
  ref_counts_ctrl,
  var_counts_ctrl,
  ref_counts_case,
  var_counts_case
)

Arguments

ref_counts_ctrl, var_counts_ctrl

Numeric vectors. Reference and variant counts of control samples.

ref_counts_case, var_counts_case

Numeric vectors. Reference and variant counts of case samples.

Value

Beta-value (beta) and p-value (p.value) of the generalised linear model comparing the fraction of heterozygous samples in cases versus controls.

Examples

LOItest_logreg(c(5, 8, 10, 3, 5, 6, 23), c(8, 8, 6, 4, 4, 10, 0),
    c(5, 0, 0, 3, 5, 1, 23), c(1, 8, 6, 2, 0, 10, 0))
#> $beta
#> [1] -1.954278
#> 
#> $p.value
#> [1] 3.152053e-05
#>