newSeqExpressionSet: Function to create a new 'SeqExpressionSet' object.

In EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq

Description

User-level function to create new objects of the class SeqExpressionSet.

Usage

newSeqExpressionSet(counts,
                    normalizedCounts = matrix(data=NA, nrow=nrow(counts), ncol=ncol(counts), dimnames=dimnames(counts)),
                    offset = matrix(data=0, nrow=nrow(counts), ncol=ncol(counts), dimnames=dimnames(counts)),
                    phenoData = annotatedDataFrameFrom(counts, FALSE),
                    featureData = annotatedDataFrameFrom(counts, TRUE),
                    ...)

Arguments

counts	A matrix containing the counts for an RNA-Seq experiment. One column for each lane and one row for each gene.
normalizedCounts	A matrix with the same dimensions of counts with the normalized counts.
offset	A matrix with the same dimensions of counts defining the offset (usually useful for normalization purposes). See the package vignette for a discussion on the offset.
phenoData	A data.frame or AnnotatedDataFrame with sample information, such as biological condition, library preparation protocol, flow-cell,...
featureData	A data.frame or AnnotatedDataFrame with feature information, such as gene length, GC-content, ...
...	Other arguments will be passed to the constructor inherited from eSet.

Value

An object of class SeqExpressionSet.

Author(s)

Davide Risso

See Also

SeqExpressionSet

Examples

counts <- matrix(data=0, nrow=100, ncol=4)
for(i in 1:4) {
counts[, i] <- rpois(100, lambda=50)
}
cond <- c(rep("A", 2), rep("B", 2))

counts <- newSeqExpressionSet(counts, phenoData=data.frame(conditions=cond))

EDASeq documentation built on Nov. 8, 2020, 8:29 p.m.