AllelicSeries (version 0.0.4.1)

COAST: COding-variant Allelic Series Test

Description

Main allelic series test. Performs both Burden and SKAT type tests, then combines the results to calculate an omnibus p-value.

Usage

COAST(
  anno,
  geno,
  pheno,
  apply_int = TRUE,
  covar = NULL,
  include_orig_skato_all = FALSE,
  include_orig_skato_ptv = FALSE,
  is_pheno_binary = FALSE,
  return_omni_only = FALSE,
  score_test = FALSE,
  weights = DEFAULT_WEIGHTS
)

Value

Numeric p-value.

Arguments

anno

(snps x 1) annotation vector with values in c(0, 1, 2).

geno

(n x snps) genotype matrix.

pheno

(n x 1) phenotype vector.

apply_int

Apply rank-based inverse normal transform to the phenotype? Default: TRUE. Ignored if phenotype is binary.

covar

(n x p) covariate matrix. Defaults to an (n x 1) intercept.

include_orig_skato_all

Include the original version of SKAT-O applied to all variants in the omnibus test? Default: FALSE.

include_orig_skato_ptv

Include the original version of SKAT-O applied to PTV variants only in the omnibus test? Default: FALSE.

is_pheno_binary

Is the phenotype binary? Default: FALSE.

return_omni_only

Return only the omnibus p-value? Default: FALSE.

score_test

Use a score test for burden analysis? If FALSE, uses a Wald test.

weights

(3 x 1) annotation category weights.

Examples

# Generate data.
data <- DGP(n = 1e3, snps = 1e2)

# Run the COding-variant Allelic Series Test.
results <- COAST(
  anno = data$anno,
  geno = data$geno,
  pheno = data$pheno,
  covar = data$covar
)
show(results)