The Seurat Class and Interaction Methods

Seurat-class Seurat

The Seurat Class

.DollarNames(<Seurat>) `$`(<Seurat>) `$<-`(<Seurat>) `[`(<Seurat>) `[[`(<Seurat>) dim(<Seurat>) dimnames(<Seurat>) head(<Seurat>) merge(<Seurat>) names(<Seurat>) subset(<Seurat>) tail(<Seurat>) `[[<-`(<Seurat>,<ANY>,<ANY>,<ANY>) colMeans(<Seurat>) colSums(<Seurat>) rowMeans(<Seurat>) rowSums(<Seurat>) show(<Seurat>)

Seurat Methods

AddMetaData()

Add in metadata associated with either cells or features.

CreateSeuratObject()

Create a Seurat object

Idents() `Idents<-`() RenameIdents() ReorderIdent() SetIdent() StashIdent() droplevels(<Seurat>) levels(<Seurat>) `levels<-`(<Seurat>)

Get, set, and manipulate an object's identity classes

Project() `Project<-`()

Get and set project information

RenameAssays()

Rename assays in a Seurat object

RenameCells()

Rename cells

UpdateSeuratObject()

Update old Seurat object to accommodate new features

as.Seurat()

Coerce to a Seurat Object

The Assay Class and Interaction Methods

Assay-class Assay

The Assay Class

`[`(<Assay>) `[[`(<Assay>) dim(<Assay>) dimnames(<Assay>) head(<Assay>) merge(<Assay>) subset(<Assay>) tail(<Assay>) `[[<-`(<Assay>,<ANY>,<ANY>,<ANY>) colMeans(<Assay>) colSums(<Assay>) rowMeans(<Assay>) rowSums(<Assay>) show(<Assay>)

Assay Methods

CreateAssayObject()

Create an Assay object

The DimReduc and JackStrawData Classes and Interaction Methods

DimReduc-class DimReduc

The Dimensional Reduction Class

`[`(<DimReduc>) `[[`(<DimReduc>) dim(<DimReduc>) dimnames(<DimReduc>) length(<DimReduc>) merge(<DimReduc>) names(<DimReduc>) print(<DimReduc>) subset(<DimReduc>) show(<DimReduc>)

DimReduc Methods

CreateDimReducObject()

Create a DimReduc object

JackStrawData-class JackStrawData

The JackStrawData Class

.DollarNames(<JackStrawData>) `$`(<JackStrawData>) as.logical(<JackStrawData>) show(<JackStrawData>)

JackStrawData Methods

JS() `JS<-`()

Get and set JackStraw information

The SeuratCommand Class and Interaction Methods

SeuratCommand-class SeuratCommand

The SeuratCommand Class

.DollarNames(<SeuratCommand>) `$`(<SeuratCommand>) `[`(<SeuratCommand>) as.list(<SeuratCommand>) show(<SeuratCommand>)

SeuratCommand Methods

LogSeuratCommand()

Log a command

The SpatialImage Class and Interaction Methods

SpatialImage-class SpatialImage

The SpatialImage class

Cells(<SpatialImage>) DefaultAssay(<SpatialImage>) `DefaultAssay<-`(<SpatialImage>) GetImage(<SpatialImage>) GetTissueCoordinates(<SpatialImage>) IsGlobal(<SpatialImage>) Key(<SpatialImage>) `Key<-`(<SpatialImage>) Radius(<SpatialImage>) RenameCells(<SpatialImage>) `[`(<SpatialImage>) dim(<SpatialImage>) subset(<SpatialImage>) show(<SpatialImage>)

SpatialImage methods

Radius()

Get the spot radius from an image

The Graph and Neighbor Classes and Interaction Methods

Graph-class Graph

The Graph Class

as.Graph()

Coerce to a Graph Object

Neighbor-class Neighbor

The Neighbor class

dim(<Neighbor>) show(<Neighbor>)

Neighbor Methods

as.Neighbor()

Coerce to a Neighbor Object

Accessing and Setting Object Data

GetAssayData() SetAssayData()

Get and Set Assay Data

Cells() Features()

Cell and Feature Names

CellsByIdentities()

Get cell names grouped by identity class

CellsByImage()

Get a vector of cell names associated with an image (or set of images)

Command()

Get SeuratCommands

DefaultAssay() `DefaultAssay<-`()

Default Assay

Distances()

Get the Neighbor nearest neighbors distance matrix

Embeddings()

Get Cell Embeddings

FetchData()

Access cellular data

GetImage()

Get image data

GetTissueCoordinates()

Get tissue coordinates

Images()

Pull spatial image names

Indices()

Get Neighbor nearest neighbor index matrices

IsGlobal()

Is an object global/persistent?

Key() `Key<-`() Keys()

Get and set object keys

Loadings() `Loadings<-`()

Get and set feature loadings

Misc() `Misc<-`()

Get and set miscellaneous data

Index() `Index<-`()

Get Neighbor algorithm index

Assays() Graphs() Neighbors() Reductions()

Query Specific Object Types

Stdev()

Get the standard deviations for an object

Tool() `Tool<-`()

Get and set additional tool data

HVFInfo() VariableFeatures() `VariableFeatures<-`() SVFInfo() SpatiallyVariableFeatures()

Highly Variable Features

Version()

Get Version Information

WhichCells()

Identify cells matching certain criteria

Utility Functions

`%iff%`

Set a default value depending on if an object is NULL

AttachDeps()

Attach Required Packages

CheckGC()

Conditional Garbage Collection

DefaultDimReduc()

Find the default DimReduc

FilterObjects()

Find Sub-objects of a Certain Class

IsMatrixEmpty()

Check if a matrix is empty

PackageCheck()

Check the existence of a package

RandomName()

Generate a random name

RowMergeSparseMatrices()

Merge Sparse Matrices by Row

UpdateSlots()

Update slots in an object

as.sparse()

Cast to Sparse

S4ToList() IsS4List() ListToS4()

S4/List Conversion

`%NA%` `%na%` `%!NA%` `%!na%`

Set if NA

Package Information

SeuratObject SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

pbmc_small

A small example version of the PBMC dataset

reexports plan colMeans colSums rowMeans rowSums handlers with_progress

Objects exported from other packages