1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
\name{DGEList}
\alias{DGEList}
\title{
DGEList Constructor
}
\description{
Creates a \code{DGEList} object from a table of counts (rows=features, columns=samples), group indicator for each column, library size (optional) and a table of feature annotation (optional).
}
\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)
}
\arguments{
\item{counts}{numeric matrix of read counts.}
\item{lib.size}{numeric vector giving the total count (sequence depth) for each library.}
\item{norm.factors}{numeric vector of normalization factors that modify the library sizes.}
\item{samples}{data frame containing information for each sample.}
\item{group}{vector or factor giving the experimental group/condition for each sample/library.}
\item{genes}{data frame containing annotation information for each gene.}
\item{remove.zeros}{logical, whether to remove rows that have 0 total count.}
}
\details{
To facilitate programming pipelines,
\code{NULL} values can be input for \code{lib.size}, \code{norm.factors}, \code{samples} or \code{group}, in which case the default value is used as if the argument had been missing.
}
\value{a \code{\link[edgeR:DGEList-class]{DGEList}} object}
\author{edgeR team. First created by Mark Robinson.}
\seealso{\code{\link[edgeR:DGEList-class]{DGEList-class}}}
\examples{
ngenes <- 1000
nsamples <- 4
Counts <- matrix(rnbinom(ngenes*nsamples,mu=5,size=2),ngenes,nsamples)
rownames(Counts) <- 1:ngenes
y <- DGEList(counts=Counts, group=rep(1:2,each=2))
dim(y)
colnames(y)
y$samples
y$genes <- data.frame(Symbol=paste0("Gene",1:ngenes))
show(y)
}
\concept{edgeR classes}
|
