newSeqExpressionSet {EDASeq} | R Documentation

## Function to create a new `SeqExpressionSet` object.

### 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))

[Package EDASeq version 2.20.0 Index]