diffData: Differential comparison data

Description Usage Arguments Details Value Note Author(s) References Examples

View source: R/methods-CuffFeature.R View source: R/methods-CuffFeatureSet.R View source: R/methods-CuffData.R

Description

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

Usage

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## 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

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

cummeRbund documentation built on May 2, 2018, 3:12 a.m.