Getter/setter methods {SingleCellExperiment} | R Documentation |
Getter/setter methods for the LinearEmbeddingMatrix class.
## S4 method for signature 'LinearEmbeddingMatrix' sampleFactors(x, withDimnames=TRUE) ## S4 replacement method for signature 'LinearEmbeddingMatrix' sampleFactors(x) <- value ## S4 method for signature 'LinearEmbeddingMatrix' featureLoadings(x, withDimnames=TRUE) ## S4 replacement method for signature 'LinearEmbeddingMatrix' featureLoadings(x) <- value ## S4 method for signature 'LinearEmbeddingMatrix' factorData(x) ## S4 replacement method for signature 'LinearEmbeddingMatrix' factorData(x) <- value ## S4 method for signature 'LinearEmbeddingMatrix' as.matrix(x, ...) ## S4 method for signature 'LinearEmbeddingMatrix' dim(x) ## S4 method for signature 'LinearEmbeddingMatrix' dimnames(x) ## S4 replacement method for signature 'LinearEmbeddingMatrix' dimnames(x) <- value ## S4 method for signature 'LinearEmbeddingMatrix' x$name ## S4 replacement method for signature 'LinearEmbeddingMatrix' x$name <- value
x |
A LinearEmbeddingMatrix object. |
value |
An appropriate value to assign to the relevant slot. |
withDimnames |
A logical scalar indicating whether dimension names should be attached to the returned object. |
name |
A string specifying a field of the |
... |
Further arguments, ignored. |
Any value
to assign to sampleFactors
and featureLoadings
should be matrix-like objects,
while factorData
should be a DataFrame - ee LinearEmbeddingMatrix for details.
The as.matrix
method will return the matrix of sample factors, consistent with the fact that the LinearEmbeddingMatrix mimics a sample-factor matrix.
However, unlike the sampleFactors
method, this is always guaranteed to return an ordinary R matrix, even if an alternative representation was stored in the slot.
This ensures consistency with as.matrix
methods for other matrix-like S4 classes.
For assignment to dimnames
, a list of length 2 should be used containing vectors of row and column names.
For the getter methods sampleFactors
, featureLoadings
and factorData
, the value of the slot with the same name is returned.
For the corresponding setter methods, a LinearEmbeddingMatrix is returned with modifications to the named slot.
For dim
, the dimensions of the sampleFactors
slot are returned in an integer vector of length 2.
For dimnames
, a list of length 2 containing the row and column names is returned.
For as.matrix
, an ordinary matrix derived from sampleFactors
is returned.
For $
, the value of the named field of the factorData
slot is returned.
For $<-
, a LinearEmbeddingMatrix is returned with the modified field in factorData
.
Keegan Korthauer, Davide Risso and Aaron Lun
example(LinearEmbeddingMatrix, echo=FALSE) # Using the class example sampleFactors(lem) sampleFactors(lem) <- sampleFactors(lem) * -1 featureLoadings(lem) featureLoadings(lem) <- featureLoadings(lem) * -1 factorData(lem) factorData(lem)$whee <- 1 nrow(lem) ncol(lem) colnames(lem) <- LETTERS[seq_len(ncol(lem))] as.matrix(lem)