Class for Gene Expression Deconvolution Benchmark Datasets

Methods

1. dimsignature(x = "ExpressionMix"): Similarly to NMF-class objects, ExpressionMix objects have a "third" dimension, the number of underlying cell types, inherited from the embedded NMF model.

   dim returns the dimensions of an ExpressionMix object. It returns a 3-length integer vector, containing the number of features, samples and components respectively.

2. dimnamessignature(x = "ExpressionMix"): dimnames returns the dimension names of an ExpressionMix object. It returns a list with 3 elements: the feature names, sample names and the constituent cell/tissue names (i.e. the basis names of the underlying NMF model).

3. dimnames<-signature(x = "ExpressionMix"): dimnames<- Sets the dimension names of an ExpressionMix object. The replacement value must be a list containing the feature names, the samples names (optional), and the constituent cell/tissue names (optional), all as character vectors of correct dimensions (i.e. compatible with the number of features, samples and constituents).

4. .DollarNamessignature(x = "ExpressionMix"): Auto-completion for ExpressionMix-class objects

5. esetsignature(object = "ExpressionMix"): Extracts an ExpressionSet object from an ExpressionMix object.

   Because ExpressionMix-class inherits from ExpressionSet-class, this methods simply returns the object coerced as an ExpressionSet object.

6. featureNames<-signature(object = "ExpressionMix"): Sets the feature names on both the ExpressionSet and NMF objects.

7. initializesignature(.Object = "ExpressionMix"): Initialize method for ExpressionMix object

8. mixDatasignature(object = "ExpressionMix"): Extracts mixture data from an ExpressionMix object.

   Because ExpressionMix-class inherits from linkS4class{NMFstd}, this methods simply returns the the object coerced as an NMFstd object.

9. mixData<-signature(object = "ExpressionMix", value = "NMFstd"): Sets mixture data in an ExpressionMix object.

   Because ExpressionMix-class inherits from linkS4class{NMFstd}, this method simply copies all slots in value in into the corresponding slots in object, and then checks that the result object is valid.

10. sampleNames<-signature(object = "ExpressionMix"): Sets the sample names on both the ExpressionSet and NMF objects.

11. showDatasignature(object = "ExpressionMix"): Shows which data is available in an ExpressionMix object.

    This method invisibly returns a 3-length logical that indicates if expression, signature and proportion data are available in object.