MiDAS-class {midasHLA} | R Documentation

## MiDAS class

### Description

The `MiDAS` class is a `MultiAssayExperiment` object containing data and metadata required for MiDAS analysis.

Valid `MiDAS` object must have unique features names across all experiments and colData. It's metadata list needs to have a `placeholder` element, which is a string specifying name of column in colData used when defining statistical model for downstream analyses (see `runMiDAS` for more details). Optionally the object's metadata can also store `'hla_calls'` and `'kir_calls'` data frames (see `prepareMiDAS` for more details).

### Usage

    ## S4 method for signature 'MiDAS'
    getExperiments(object)

    ## S4 method for signature 'MiDAS'
    getHlaCalls(object)

    ## S4 method for signature 'MiDAS'
    getKirCalls(object)

    ## S4 method for signature 'MiDAS'
    getPlaceholder(object)

    ## S4 method for signature 'MiDAS'
    getOmnibusGroups(object, experiment)

    ## S4 method for signature 'MiDAS'
    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)
    )

    ## S4 method for signature 'MiDAS'
    filterByFrequency(
      object,
      experiment,
      lower_frequency_cutoff = NULL,
      upper_frequency_cutoff = NULL,
      carrier_frequency = FALSE
    )

    ## S4 method for signature 'MiDAS'
    filterByOmnibusGroups(object, experiment, groups)

    ## S4 method for signature 'MiDAS'
    filterByVariables(object, experiment, variables)

    ## S4 method for signature 'MiDAS'
    getAllelesForAA(object, aa_pos)

### Arguments

`object` | `MiDAS` object.
`experiment` | String specifying experiment.
`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.
`lower_frequency_cutoff` | Number giving lower frequency threshold. Numbers greater than 1 are interpreted as the number of feature occurrences, numbers between 0 and 1 as fractions.
`upper_frequency_cutoff` | Number giving upper frequency threshold. Numbers greater than 1 are interpreted as the number of feature occurrences, numbers between 0 and 1 as fractions.
`groups` | Character vector specifying omnibus groups to select. See `getOmnibusGroups` for more details.
`variables` | Character vector specifying features to select.
`aa_pos` | String specifying gene and amino acid position, example `"A_9"`.

### Value

Instance of class MiDAS

[Package midasHLA version 1.2.0 Index]