Exploratory Analysis {cummeRbund} | R Documentation

## Methods for Exploratory Analysis in cummeRbund

### Description

Exploratory analysis methods for cummeRbund RNA-Seq data.

### Usage

    ## S4 method for signature 'CuffData'
    csNMF(object,k,logMode=T,pseudocount=1,maxiter=1000,replicates=FALSE,fullnames=FALSE)
    ## S4 method for signature 'CuffFeatureSet'
    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]

### 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.

### Value

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

### Note

None.

### Author(s)

Loyal A. Goff

### References

None.

### Examples

    	data(sampleData)
    	csNMF(sampleGeneSet,4)

[Package cummeRbund version 2.29.0 Index]