seurat-SingleCellExperiment: Extend S4 Methods for 'seurat' Class

In roryk/bcbioSinglecell: Single-Cell RNA-Seq Utilities

Description

Provide limited SingleCellExperiment-like method support.

Usage

## S4 method for signature 'seurat'
cell2sample(object)

## S4 method for signature 'seurat'
plotCellCounts(object, interestingGroups, fill = NULL,
  title = "cell counts")

## S4 method for signature 'seurat,ANY'
assay(x)

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

## S4 method for signature 'seurat'
colnames(x)

## S4 method for signature 'seurat'
counts(object)

## S4 method for signature 'seurat'
metadata(x)

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

## S4 method for signature 'seurat'
rowData(x)

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

## S4 method for signature 'seurat'
rownames(x)

## S4 method for signature 'seurat'
gene2symbol(object)

## S4 method for signature 'seurat'
interestingGroups(object)

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

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

Arguments

object	Object.
interestingGroups	Character vector of interesting groups. Must be formatted in camel case and intersect with sampleData() colnames.
fill	Desired ggplot fill scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_fill_manual().
title	Plot title.
x	Primary object.
value	Object to assign.
normalized	Normalized (TRUE) or raw (FALSE) counts.

Value

Match SummarizedExperiment method return.

Author(s)

Michael Steinbaugh

See Also

getMethod("metadata<-", "Annotated")

roryk/bcbioSinglecell documentation built on May 27, 2019, 10:44 p.m.