newMRexperiment: Create a MRexperiment object

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Create a MRexperiment object

Description

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

Usage

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

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

HCBravoLab/metagenomeSeq documentation built on Dec. 20, 2024, 4:06 p.m.