base-Seurat: Extend base S4 methods for 'Seurat' class

In steinbaugh/pointillism: Single-cell RNA-seq toolkit

Extend base S4 methods for Seurat class

Description

Provide limited SingleCellExperiment-like method support.

Usage

## S4 method for signature 'Seurat'
GeneToSymbol(object, ...)

## S4 method for signature 'Seurat,ANY'
assay(x, i, withDimnames = TRUE, ...)

## S4 method for signature 'Seurat'
assayNames(x, ...)

## S4 method for signature 'Seurat'
assays(x, withDimnames = TRUE, ...)

## S4 method for signature 'Seurat'
cellCountsPerCluster(object, ...)

## S4 method for signature 'Seurat'
clusters(object)

## S4 method for signature 'Seurat'
colData(x)

## S4 replacement method for signature 'Seurat,DFrame'
colData(x) <- value

## S4 method for signature 'Seurat'
counts(object, assay = NULL)

## S4 method for signature 'Seurat'
cpm(object, assay = NULL)

## S4 method for signature 'Seurat'
diffExp(object, ...)

## S4 method for signature 'Seurat'
diffExpPerCluster(object, ...)

## S4 method for signature 'Seurat'
findMarkers(object, ...)

## S4 method for signature 'Seurat'
interestingGroups(object, ...)

## S4 replacement method for signature 'Seurat,character'
interestingGroups(object) <- value

## S4 method for signature 'Seurat'
logcounts(object, assay = NULL)

## S4 method for signature 'Seurat'
mapGenesToIds(object, genes, strict = TRUE)

## S4 method for signature 'Seurat'
mapGenesToRownames(object, genes, strict = TRUE)

## S4 method for signature 'Seurat'
mapGenesToSymbols(object, genes, strict = TRUE)

## S4 method for signature 'Seurat'
metadata(x, ...)

## S4 replacement method for signature 'Seurat'
metadata(x) <- value

## S4 method for signature 'Seurat'
metrics(object, ...)

## S4 method for signature 'Seurat'
normalize(object)

## S4 method for signature 'Seurat'
normcounts(object, assay = NULL)

## S4 method for signature 'Seurat'
organism(object)

## S4 replacement method for signature 'Seurat'
organism(object) <- value

## S4 method for signature 'Seurat'
plotCellCountsPerCluster(object, ...)

## S4 method for signature 'Seurat,KnownMarkers'
plotCellTypesPerCluster(object, markers, ...)

## S4 method for signature 'Seurat'
plotCounts(object, ...)

## S4 method for signature 'Seurat'
plotDots(object, ...)

## S4 method for signature 'Seurat'
plotFeature(object, ...)

## S4 method for signature 'Seurat,KnownMarkers'
plotKnownMarkers(object, markers, ...)

## S4 method for signature 'Seurat'
plotMarker(object, ...)

## S4 method for signature 'Seurat'
plotPca(object, ...)

## S4 method for signature 'Seurat'
plotReducedDim(object, ...)

## S4 method for signature 'Seurat'
plotStackedBarPlot(object, ...)

## S4 method for signature 'Seurat'
plotTsne(object, ...)

## S4 method for signature 'Seurat'
plotViolin(object, ...)

## S4 method for signature 'Seurat'
plotUmap(object, ...)

## S4 method for signature 'Seurat,ANY'
reducedDim(x, type = 1L, withDimnames = TRUE)

## S4 method for signature 'Seurat'
reducedDimNames(x)

## S4 method for signature 'Seurat'
reducedDims(x, ...)

## S4 method for signature 'Seurat'
rowData(x, use.names = TRUE, ...)

## S4 method for signature 'Seurat'
rowRanges(x)

## S4 replacement method for signature 'Seurat,ANY'
rowRanges(x) <- value

## S4 method for signature 'Seurat'
sampleData(object, ...)

## S4 replacement method for signature 'Seurat,DFrame'
sampleData(object) <- value

## S4 method for signature 'Seurat'
sampleNames(object)

Arguments

object	Object.
...	Additional arguments.
x	Object.
i	Indices specifying elements to extract or replace. Indices are numeric or character vectors, empty (missing), or NULL. For more information: help(topic = "Extract", package = "base")
value	Value to assign.
assay	vector(1). Assay name or index position.
genes	character. Gene identifiers.

Value

Varies, depending on the generic.

Note

Updated 2023-08-16.

See Also

• SeuratObject::LayerData().

steinbaugh/pointillism documentation built on Oct. 13, 2023, 10:43 p.m.