diffData {cummeRbund} | R Documentation |
An accessor method to retrieve differential expression data from a 'CuffData', 'CuffFeatureSet', or 'CuffFeature' object
## S4 method for signature 'CuffData' diffData(object, x, y, features=FALSE) ## S4 method for signature 'CuffData' diffTable(object,logCutoffValue=99999)
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. |
None
A data.frame object
None
Loyal A. Goff
None
data(sampleData) diff<-diffData(sampleGeneSet) #returns a dataframe of differential expression data from sample CuffGeneSet object.