getHlaKirInteractions {midasHLA} | R Documentation

## Get HLA - KIR interactions

### Description

`getHlaKirInteractions` calculate presence-absence matrix of HLA - KIR interactions.

### Usage

    getHlaKirInteractions(
      hla_calls,
      kir_calls,
      interactions_dict = system.file("extdata", "Match_counts_hla_kir_interactions.txt",
        package = "midasHLA")
    )

### Arguments

`hla_calls` | HLA calls data frame, as returned by `readHlaCalls` function.
`kir_calls` | KIR calls data frame, as returned by `readKirCalls` function.
`interactions_dict` | Path to HLA - KIR interactions dictionary.

### Details

`hla_calls` are first reduced to all possible resolutions and converted to additional variables, such as G groups, using dictionaries shipped with the package.

`interactions_dict` file should be a tsv format with header and two columns. First column should be named `"Name"` and hold interactions names, second should be named `"Expression"` and hold expression used to identify interaction (eg. `"C2 & KIR2DL1"` will match all samples with `C2` and `KIR2DL1`). The package is shipped with an interactions file based on Pende et al., 2019.

### Value

Data frame with variable number of columns. First column named `"ID"` corresponds to `"ID"` column in `counts`, further columns hold indicators for HLA - KIR interactions. `1` and `0` code presence and absence of a variable respectively.

### Examples

    getHlaKirInteractions(
      hla_calls = MiDAS_tut_HLA,
      kir_calls = MiDAS_tut_KIR,
      interactions_dict = system.file(
        "extdata", "Match_counts_hla_kir_interactions.txt",
        package = "midasHLA")
    )

[Package midasHLA version 1.2.0 Index]