applyInheritanceModel {midasHLA} | R Documentation

## 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.

[Package midasHLA version 1.2.0 Index]