diffData: Differential comparison data

In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing 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.

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.