Create a MRexperiment object

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Description

This function creates a MRexperiment object from a matrix or data frame of count data.

Usage

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newMRexperiment(counts, phenoData = NULL, featureData = NULL,
  libSize = NULL, normFactors = NULL)

Arguments

counts

A matrix or data frame of count data. The count data is representative of the number of reads annotated for a feature (be it gene, OTU, species, etc). Rows should correspond to features and columns to samples.

phenoData

An AnnotatedDataFrame with pertinent sample information.

featureData

An AnnotatedDataFrame with pertinent feature information.

libSize

libSize, library size, is the total number of reads for a particular sample.

normFactors

normFactors, the normalization factors used in either the model or as scaling factors of sample counts for each particular sample.

Details

See MRexperiment-class and eSet (from the Biobase package) for the meaning of the various slots.

Value

an object of class MRexperiment

Author(s)

Joseph N Paulson

Examples

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cnts = matrix(abs(rnorm(1000)),nc=10)
obj <- newMRexperiment(cnts)

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