DGEList: DGEList Constructor Generic

In aoles/DEFormats: Differential gene expression data formats converter

DGEList Constructor Generic

Description

Creates a DGEList object.

Usage

DGEList(counts, ...)

## S4 method for signature 'RangedSummarizedExperiment'
DGEList(
  counts = new("RangedSummarizedExperiment"),
  lib.size = colData(counts)$lib.size,
  norm.factors = colData(counts)$norm.factors,
  samples = colData(counts),
  group = NULL,
  genes = as.data.frame(rowRanges(counts)),
  remove.zeros = FALSE
)

Arguments

counts	read counts, either a numeric matrix or a RangedSummarizedExperiment object.
...	other arguments are not currently used.
lib.size	numeric vector of library sizes (sequencing depths) for the samples. Defaults to colSums(counts).
norm.factors	numeric vector of normalization factors that modify the library sizes. Defaults to a vector of ones.
samples	data.frame containing sample information, with a row for each sample. This data.frame will be appended to the samples component of the DGEList object.
group	vector or factor giving the experimental group or treatment condition for each sample. Defaults to a single group.
genes	data.frame containing gene annotation.
remove.zeros	logical, whether to remove rows that have 0 total count.

Value

A DGEList object.

Author(s)

Andrzej Oleś <[e-mail]>, 2016-2023

Examples

se = simulateRnaSeqData(output = "RangedSummarizedExperiment")

## Initialize a DGEList from a RangedSummarizedExperiment object
DGEList(se)

aoles/DEFormats documentation built on April 18, 2023, 12:07 a.m.