MPRASet-class {mpra} | R Documentation

## Class `"MPRASet"`

### Description

A container for data from massively parallel reporter assays (MPRA). Builds on the SummarizedExperiment class.

### Usage

    ## Constructor
    MPRASet(DNA = new("matrix"), RNA = new("matrix"),
            barcode = new("character"), eid = new("character"),
            eseq = new("character"), ...)

    ## Accessors
    getRNA(object, aggregate = FALSE)
    getDNA(object, aggregate = FALSE)
    getBarcode(object)
    getEid(object)
    getEseq(object)

### Arguments

`object` | A `MPRASet` object.
`aggregate` | A `logical` indicating if data should be aggregated to the element level (by summing across barcodes).
`DNA` | A matrix of DNA counts where rows correspond to elements or individual barcodes and columns to samples of conditions being compared.
`RNA` | A matrix of RNA counts where rows correspond to elements or individual barcodes and columns to samples of conditions being compared.
`barcode` | If barcodes are supplied, a `character` vector of length equal to the number of rows in `DNA` and `RNA` containing the barcode sequences or identifiers. `NULL` otherwise.
`eid` | A `character` vector of length equal to the number of rows in `DNA` and `RNA` containing the enhancer identifiers corresponding to each row.
`eseq` | If supplied, a `character` vector of length equal to the number of rows in `DNA` and `RNA` containing the enhancer sequences corresponding to the regulatory elements in each row. `NULL` otherwise.
`...` | Further arguments to be passed to `SummarizedExperiment`.

### Value

The constrcutor function `MPRASet` returns an object of class `"MPRASet"`.

### Slots

Slots are as described in a `SummarizedExperiment`. Of particular interest are `colData` which describes the phenotype data. The `assay` slot holds the assay data, with specific assay names `RNA` and `DNA` (accessed by `getRNA` and `getDNA`). Element and barcode data are accessible in the `rowData` slot. We have chosen to store barcode and element as `character` to be flexible, although they are often DNA sequences (and could therefore be considered `DNAStringSet` (from package Biostrings)).

### Extends

Class `"SummarizedExperiment"`, directly.

### Accessors

`getDNA`:

  Gets the DNA channel data.

`getRNA`:

  Gets the RNA channel data.

`getBarcode`:

  Gets the barcode, if present.

`getEid`:

  Gets the element ID

`getEseq`:

  Gets the element sequence, if present.

### See Also

`SummarizedExperiment` for the basic class that is used as a building block.

### Examples

    showClass("MPRASet")

[Package mpra version 1.12.1 Index]