applyInheritanceModel: Apply inheritance model

In Genentech/MiDAS: R package for immunogenomics data handling and association analysis

Apply inheritance model

Description

Helper function transforming experiment counts to selected inheritance_model.

Usage

applyInheritanceModel(
  experiment,
  inheritance_model = c("dominant", "recessive", "additive", "overdominant")
)

## S3 method for class 'matrix'
applyInheritanceModel(
  experiment,
  inheritance_model = c("dominant", "recessive", "additive", "overdominant")
)

## S3 method for class 'SummarizedExperiment'
applyInheritanceModel(
  experiment,
  inheritance_model = c("dominant", "recessive", "additive", "overdominant")
)

Arguments

experiment	Matrix or SummarizedExperiment object.
inheritance_model	String specifying inheritance model to use. Available choices are "dominant", "recessive", "additive".

Details

Under "dominant" model homozygotes and heterozygotes are coded as 1. In "recessive" model homozygotes are coded as 1 and other as 0. In "additive" model homozygotes are coded as 2 and heterozygotes as 1. In "overdominant" homozygotes (both 0 and 2) are coded as 0 and heterozygotes as 1.

Value

experiment converted to specified inheritance model.

Genentech/MiDAS documentation built on Feb. 5, 2024, 11:52 a.m.