getHlaFrequencies {midasHLA} | R Documentation

## Calculate HLA allele frequencies

### Description

`getHlaFrequencies` calculates allele frequencies in HLA calls data frame.

### Usage

    getHlaFrequencies(
      hla_calls,
      carrier_frequency = FALSE,
      compare = FALSE,
      ref_pop = c("USA NMDP African American pop 2", "USA NMDP Chinese",
        "USA NMDP European Caucasian", "USA NMDP Hispanic South or Central American",
        "USA NMDP Japanese", "USA NMDP North American Amerindian",
        "USA NMDP South Asian Indian"),
      ref = allele_frequencies
    )

### Arguments

`hla_calls` | HLA calls data frame, as returned by `readHlaCalls` function.
`carrier_frequency` | Logical flag indicating if carrier frequency should be returned.
`compare` | Logical flag indicating if `hla_calls` frequencies should be compared to reference frequencies given in `ref`.
`ref_pop` | Character vector giving names of reference populations in `ref` to compare with. Optionally vector can be named, then those names will be used as population names.
`ref` | Data frame giving reference allele frequencies. See `allele_frequencies` for an example.

### Details

Both gene copies are taken into consideration for frequencies calculation, `frequency = n / (2 * j)` where `n` is the number of allele occurrences and `j` is the number of samples in `hla_calls`.

### Value

Data frame with each row holding HLA allele, it's count and frequency.

### Examples

    getHlaFrequencies(MiDAS_tut_HLA)

[Package midasHLA version 1.2.0 Index]