newMRexperiment {metagenomeSeq} | R Documentation |
This function creates a MRexperiment object from a matrix or data frame of count data.
newMRexperiment( counts, phenoData = NULL, featureData = NULL, libSize = NULL, normFactors = NULL )
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. |
See MRexperiment-class
and eSet
(from the Biobase
package) for the meaning of the various slots.
an object of class MRexperiment
Joseph N Paulson
cnts = matrix(abs(rnorm(1000)),nc=10) obj <- newMRexperiment(cnts)