MPRASet-class: Class '"MPRASet"'

In hansenlab/mpra: Analyze massively parallel reporter assays

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")

hansenlab/mpra documentation built on Sept. 15, 2024, 4:11 p.m.