DEFormats (version 1.0.2)

DGEList: DGEList Constructor Generic

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)
 "DGEList"(counts = new("RangedSummarizedExperiment"), lib.size = colData(counts)$lib.size, norm.factors = colData(counts)$norm.factors, samples = colData(counts), group = colData(counts)$group, 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.

Examples

se = simulateRnaSeqData(output = "RangedSummarizedExperiment")

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