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

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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

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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))


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