SE2DGEList: SummarizedExperiment to DGEList

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Given any SummarizedExperiment data object, extract basic information needed and convert it into a DGEList object.

Usage

SE2DGEList(object)

Arguments

object

a SummarizedExperiment object. Must have counts in its assay component.

Details

This function takes a SummarizedExperiment data object as input. The counts of the assay component of the input SummarizedExperiment data object is extracted and used as the counts component of the output DGEList object. The rowRanges or rowData of the input is converted into a data.frame and used as genes in the output. The colData of the input is also converted into a data.frame and used as the sample information in the output.

Value

A DGEList object.

Author(s)

Yunshun Chen and Gordon Smyth

Examples

## Not run: 
library(SummarizedExperiment)
example(SummarizedExperiment)
y <- SE2DGEList(se)

## End(Not run)

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.