MPRASet-class: Class '"MPRASet"'
In hansenlab/mpra: Analyze massively parallel reporter assays

Description Usage Arguments Value Slots Extends Accessors See Also Examples

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

## 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)

`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`.

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

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)).