LEM-getset: LinearEmbeddingMatrix getters/setters

In SingleCellExperiment: S4 Classes for Single Cell Data

Description

Getter/setter methods for the LinearEmbeddingMatrix class.

Usage

## 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

Arguments

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 factorData slot.
...	Further arguments, ignored.

Details

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.

Value

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.

Author(s)

Keegan Korthauer, Davide Risso and Aaron Lun

See Also

LinearEmbeddingMatrix

Examples

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)

SingleCellExperiment documentation built on Nov. 8, 2020, 7:51 p.m.