# phers

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`phers` is an R package for calculating phenotype risk scores, which
quantify the extent to which a person’s clinical diagnoses resemble a
given Mendelian disease. For details on the R package, see [Aref et
al. (2022)](https://doi.org/10.1093/bioinformatics/btac619). For details
on the original application of phenotype risk scores, see [Bastarache et
al. (2018)](https://pubmed.ncbi.nlm.nih.gov/29590070/).

## Installation

### Option 1: CRAN

``` r
install.packages('phers')
```

### Option 2: Hughey Lab Drat Repository

1.  Install
    [`BiocManager`](https://cran.r-project.org/package=BiocManager).

    ``` r
    if (!requireNamespace('BiocManager', quietly = TRUE))
      install.packages('BiocManager')
    ```

2.  If you use RStudio, go to Tools → Global Options… → Packages → Add…
    (under Secondary repositories), then enter:

    - Name: hugheylab
    - Url: <https://hugheylab.github.io/drat/>

    You only have to do this once. Then you can install or update the
    package by entering:

    ``` r
    BiocManager::install('phers')
    ```

    Alternatively, you can install or update the package by entering:

    ``` r
    BiocManager::install('phers', site_repository = 'https://hugheylab.github.io/drat/')
    ```

## Usage

Check out the [reference
documentation](https://phers.hugheylab.org/reference/index.html).

# Package index

## All functions

- [`demoSample`](https://phers.hugheylab.org/reference/demoSample.md) :
  Sample table of demographic information
- [`diseaseDxIcdMap`](https://phers.hugheylab.org/reference/diseaseDxIcdMap.md)
  : Mapping of diseases and diagnostic ICD codes
- [`diseaseHpoMap`](https://phers.hugheylab.org/reference/diseaseHpoMap.md)
  : Mapping of Mendelian diseases and their clinical features
- [`getDxStatus()`](https://phers.hugheylab.org/reference/getDxStatus.md)
  : Identify cases and controls for Mendelian diseases
- [`getGeneticAssociations()`](https://phers.hugheylab.org/reference/getGeneticAssociations.md)
  : Perform association tests between phenotype risk scores and
  genotypes
- [`getPhecodeOccurrences()`](https://phers.hugheylab.org/reference/getPhecodeOccurrences.md)
  : Map ICD code occurrences to phecode occurrences
- [`getResidualScores()`](https://phers.hugheylab.org/reference/getResidualScores.md)
  : Calculate residual phenotype risk scores
- [`getScores()`](https://phers.hugheylab.org/reference/getScores.md) :
  Calculate phenotype risk scores
- [`getWeights()`](https://phers.hugheylab.org/reference/getWeights.md)
  : Calculate phecode-specific weights for phenotype risk scores
- [`hpoPhecodeMap`](https://phers.hugheylab.org/reference/hpoPhecodeMap.md)
  : Mapping of HPO terms and phecodes
- [`icdPhecodeMap`](https://phers.hugheylab.org/reference/icdPhecodeMap.md)
  : Mapping of ICD codes and phecodes
- [`icdSample`](https://phers.hugheylab.org/reference/icdSample.md) :
  Sample table of ICD occurrences
- [`mapDiseaseToPhecode()`](https://phers.hugheylab.org/reference/mapDiseaseToPhecode.md)
  : Map diseases to phecodes via HPO terms
- [`preCalcWeights`](https://phers.hugheylab.org/reference/preCalcWeights.md)
  : Pre-calculated weights for calculating phenotype risk scores