cummeRbund (version 2.14.0)

Exploratory Analysis: Methods for Exploratory Analysis in cummeRbund

Description

Exploratory analysis methods for cummeRbund RNA-Seq data.

Usage

"csNMF"(object,k,logMode=T,pseudocount=1,maxiter=1000,replicates=FALSE,fullnames=FALSE)
"csNMF"(object,k,logMode=T,pseudocount=1,maxiter=1000,replicates=FALSE,fullnames=FALSE)

Arguments

object

The output of class CuffData or CuffFeatureSet from which to draw expression estimates. (e.g. genes(cuff) or custom feature set via getGenes() or getFeatures() )

k

rank value for factorization

logMode

Logical value whether or not to use log-transformed FPKM values. [Default: TRUE]

pseudocount

Value added to FPKM to avoid log transformation issues.

maxiter

Maximum number of iterations for factorization [Default: 1000]

replicates

A logical value to indicate whether or not individual replicate expression estimates will be used.

fullnames

Logical passthrough value to fpkmMatrix whether or not to concatenate gene_short_name with tracking_id. [Default: FALSE]

Value

csNMF returns W, H - decomposed matrices of input FPKM values. (See package:NMFN for details)

Details

csNMF is a convenience method to invoke the nnmf() method from package:NMFN. This performs non-negative matrix factorization on the provided data and can be useful for many downstream applications.

References

None.

Examples

	data(sampleData)
	csNMF(sampleGeneSet,4)