Aggregator: Aggregator

In AllelicSeries: Allelic Series Test

Aggregator

Description

Aggregates genotypes within annotation categories.

Usage

Aggregator(
  anno,
  geno,
  drop_empty = TRUE,
  indicator = FALSE,
  method = "none",
  min_mac = 0,
  weights = c(1, 2, 3)
)

Arguments

anno	(snps x 1) annotation vector with integer values in 1 through the number of annotation categories L.
geno	(n x snps) genotype matrix.
drop_empty	Drop empty columns? Default: TRUE.
indicator	Convert raw counts to indicators? Default: FALSE.
method	Method for aggregating across categories: ("none", "max", "sum"). Default: "none".
min_mac	Minimum minor allele count for inclusion. Default: 0.
weights	(L x 1) vector of annotation category weights. Note that the number of annotation categories L is inferred from the length of weights.

Value

(n x L) Numeric matrix without weighting, (n x 1) numeric matrix with weighting.

Notes

• Ensure the length of the weights vector matches the total number of annotation categories.

• The weights essentially scales the minor allele count in the lth category by weights[l].

AllelicSeries documentation built on April 3, 2025, 7:46 p.m.