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\name{DGEList}
\alias{DGEList}
\alias{DGEList.default}
\alias{DGEList.data.frame}
\title{
Create a DGEList object
}
\description{
Assembles a \code{DGEList} object from its components, especially the table counts as a matrix or data.frame.
}
\usage{
\method{DGEList}{default}(counts, lib.size = NULL, norm.factors = NULL,
samples = NULL, group = NULL, genes = NULL,
remove.zeros = FALSE, \dots)
\method{DGEList}{data.frame}(counts, lib.size = NULL, norm.factors = NULL,
samples = NULL, group = NULL, genes = NULL,
remove.zeros = FALSE, annotation.columns = NULL, \dots)
}
\arguments{
\item{counts}{numeric matrix or data.frame containing sequence read counts, with rows corresponding to genes (genomic features) and columns to samples. Negative values or NAs are not allowed.}
\item{lib.size}{numeric vector of library sizes (sequencing depths) for the samples. Defaults to \code{colSums(counts)}.}
\item{norm.factors}{numeric vector of normalization factors that modify the library sizes. Defaults to a vector of ones.}
\item{samples}{data.frame containing sample information, with a row for each sample. This data.frame will be appended to the \code{samples} component of the DGEList object.}
\item{group}{vector or factor giving the experimental group or treatment condition for each sample. Defaults to a single group.}
\item{genes}{data.frame containing gene annotation.}
\item{remove.zeros}{logical, whether to remove rows that have 0 total count.}
\item{annotation.columns}{specify columns of \code{counts} that contain gene annotation rather than counts. Can be a vector of column numbers, or a vector of column names, or a logical vector.}
\item{\dots}{other arguments are not currently used.}
}
\details{
Assembles a DGEList object from its components.
The only compulsory argument is the table of counts.
Normally, \code{counts} is a numeric matrix of counts but a data.frame is also allowed.
If the \code{counts} is a data.frame, then the columns of the data.frame containing gene IDs or other gene annotation can be specified by \code{annotation.columns}, and the other columns are assumed to contain sequence read counts.
If \code{annotation.columns} is not specified, then the function will check for non-numeric columns of \code{counts}
and will attempt to set the leading columns up to the last non-numeric column as annotation.
}
\value{A \code{\link[edgeR:DGEList-class]{DGEList}} object.}
\author{edgeR team. Originally created by Mark Robinson.}
\seealso{\code{\link[edgeR:DGEList-class]{DGEList-class}}}
\examples{
ngenes <- 100
nsamples <- 4
Counts <- matrix(rnbinom(ngenes*nsamples,mu=5,size=10),ngenes,nsamples)
rownames(Counts) <- 1:ngenes
colnames(Counts) <- paste0("S",1:4)
Group <- gl(2,2)
Genes <- data.frame(Symbol=paste0("Gene",1:ngenes))
y <- DGEList(counts=Counts, group=Group, genes=Genes)
dim(y)
colnames(y)
y$samples
show(y)
}
\concept{edgeR classes}
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