getFrequencies {midasHLA} | R Documentation

## Calculate features frequencies for a given experiment in MiDAS object.

### Description

Calculate features frequencies for a given experiment in MiDAS object.

### Usage

    getFrequencies(
      object,
      experiment,
      carrier_frequency = FALSE,
      compare = FALSE,
      ref_pop = list(hla_alleles = 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"), kir_genes = c("USA California African American KIR",
        "USA California Asian American KIR", "USA California Caucasians KIR",
        "USA California Hispanic KIR")),
      ref = list(hla_alleles = allele_frequencies, kir_genes = kir_frequencies)
    )

### Arguments

`object` | `MiDAS` object.
`experiment` | Matrix or SummarizedExperiment object.
`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` | Named list of character vectors giving names of reference populations in `ref` to compare with. Optionally vectors can be named, then those names will be used as population names. Each vector should correspond to a specific experiment.
`ref` | Named list of reference frequencies data frames. Each element should give reference for a specific experiment. See `allele_frequencies` for an example on how reference frequency data frame should be formatted.

### Value

Data frame with features from selected experiment and their corresponding frequencies. Column `"term"` hold features names, `"Counts"` hold number of feature occurrences, `"Freq"` hold feature frequencies. If argument `compare` is set to `TRUE`, further columns will hold frequencies in reference populations.

### Examples

    # using default reference populations
    getFrequencies(object = MiDAS_tut_object,
                   experiment = "hla_alleles",
                   compare = TRUE)

    # using customized set of reference populations
    getFrequencies(
      object = MiDAS_tut_object,
      experiment = "hla_alleles",
      compare = TRUE,
      ref_pop = list(
        hla_alleles = c("USA NMDP Chinese", "USA NMDP European Caucasian")
      ),
      ref = list(hla_alleles = allele_frequencies)
    )

[Package midasHLA version 1.2.0 Index]