diffData {cummeRbund} | R Documentation

## Differential comparison data

### Description

An accessor method to retrieve differential expression data from a 'CuffData', 'CuffFeatureSet', or 'CuffFeature' object

### Usage

    ## S4 method for signature 'CuffData'
    diffData(object, x, y, features=FALSE)
    ## S4 method for signature 'CuffData'
    diffTable(object,logCutoffValue=99999)

### Arguments

`object` | An object of class ('CuffData' or 'CuffFeatureSet')
`x` | Optional, if x and y are both missing, data for all pairwise differential comparisons are returned, otherwise if x and y are sample names from the 'samples' table, than only differential data pertaining to those two samples are returned.
`y` | See 'x'
`features` | A logical value that returns all feature-level data as part of data.frame when true. object must be of class 'CuffData'.
`logCutoffValue` | Cutoff value for FC estimates to convert to [-]Inf values. Should never really be needed...
`...` | Additional arguments.

### Details

None

### Value

A data.frame object

### Note

None

### Author(s)

Loyal A. Goff

### References

None

### Examples

    	data(sampleData)
    	diff<-diffData(sampleGeneSet) #returns a dataframe of differential expression data from sample CuffGeneSet object.

[Package cummeRbund version 2.28.0 Index]