DGEList: DGEList Constructor Generic

In DEFormats: Differential gene expression data formats converter

Description

Creates a DGEList object.

Usage

DGEList(counts = matrix(0, 0, 0), lib.size = colSums(counts),
  norm.factors = rep(1, ncol(counts)), samples = NULL, group = NULL,
  genes = NULL, remove.zeros = FALSE)


  ## 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.
lib.size	numeric vector giving the total count (sequence depth) for each library.
norm.factors	numeric vector of normalization factors that modify the library sizes.
samples	data frame containing information for each sample.
group	vector or factor giving the experimental group/condition for each sample/library.
genes	data frame containing annotation information for each gene.
remove.zeros	logical, whether to remove rows that have 0 total count.

Value

A DGEList object.

Author(s)

Andrzej Ole<c5><9b> <[e-mail]>, 2016-2017

Examples

se = simulateRnaSeqData(output = "RangedSummarizedExperiment")

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

DEFormats documentation built on Nov. 8, 2020, 5:31 p.m.