# Data Structures for Single Cell Data

## Documentation for package ‘SeuratObject’ version 5.4.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M N O P R S T U V W misc

SeuratObject-package | SeuratObject: Data Structures for Single Cell Data

## -- A --

AddMetaData | Add in metadata associated with either cells or features.
AddMetaData.Assay | Add in metadata associated with either cells or features.
AddMetaData.Assay5 | Add in metadata associated with either cells or features.
AddMetaData.Seurat | Add in metadata associated with either cells or features.
AddSamples | Merge Seurat Objects
as.Centroids | Convert Segmentation Layers
as.Centroids.Segmentation | Convert Segmentation Layers
as.Graph | Coerce to a 'Graph' Object
as.Graph.Matrix | Coerce to a 'Graph' Object
as.Graph.matrix | Coerce to a 'Graph' Object
as.Graph.Neighbor | Coerce to a 'Graph' Object
as.list.SeuratCommand | Coerce a 'SeuratCommand' to a list
as.logical.JackStrawData | 'JackStrawData' Methods
as.matrix.LogMap | Coerce Logical Maps to Matrices
as.Neighbor | Coerce to a 'Neighbor' Object
as.Neighbor.Graph | Coerce to a 'Neighbor' Object
as.Segmentation | Convert Segmentation Layers
as.Segmentation.Centroids | Convert Segmentation Layers
as.Seurat | Coerce to a 'Seurat' Object
as.sparse | Cast to Sparse
as.sparse.data.frame | Cast to Sparse
as.sparse.Matrix | Cast to Sparse
as.sparse.matrix | Cast to Sparse
as.sparse.ngCMatrix | Cast to Sparse
Assay | The Assay Class
Assay-class | The Assay Class
Assay-validity | V3 Assay Validity
Assay5 | The v5 'Assay' Object
Assay5-class | The v5 'Assay' Object
Assay5-validity | V5 Assay Validity
AssayData | Get and Set Assay Data
Assays | Query Specific Object Types
Assays.Seurat | Query Specific Object Types
AttachDeps | Attach Required Packages

## -- B --

Boundaries | Get, Set, and Query Segmentation Boundaries
Boundaries.FOV | Get, Set, and Query Segmentation Boundaries

## -- C --

CastAssay | Cast Assay Layers
CastAssay.Assay5 | Cast Assay Layers
Cells | Cell and Feature Names
Cells.Assay5 | Cell and Feature Names
Cells.Centroids | 'Centroids' Methods
Cells.default | Cell and Feature Names
Cells.DimReduc | Cell and Feature Names
Cells.FOV | 'FOV' Methods
Cells.Neighbor | Cell and Feature Names
Cells.Segmentation | 'Segmentation' Methods
Cells.SpatialImage | 'SpatialImage' methods
CellsByIdentities | Get cell names grouped by identity class
CellsByImage | Get a vector of cell names associated with an image (or set of images)
Centroids-class | The 'Centroids' Class
Centroids-methods | 'Centroids' Methods
CheckGC | Conditional Garbage Collection
CheckLayersName | Check layers names for the input list
Command | Get SeuratCommands
Command.Seurat | Get SeuratCommands
coordinates-method | 'Segmentation' Methods
CreateAssay5Object | Create a v5 Assay object
CreateAssayObject | Create an Assay object
CreateCentroids | Create a 'Centroids' Objects
CreateDimReducObject | Create a DimReduc object
CreateFOV | Create Spatial Coordinates
CreateFOV.Centroids | Create Spatial Coordinates
CreateFOV.data.frame | Create Spatial Coordinates
CreateFOV.list | Create Spatial Coordinates
CreateFOV.Segmentation | Create Spatial Coordinates
CreateMolecules | Create a 'Molecules' Object
CreateMolecules.data.frame | Create a 'Molecules' Object
CreateMolecules.Molecules | Create a 'Molecules' Object
CreateMolecules.NULL | Create a 'Molecules' Object
CreateSegmentation | Create a 'Segmentation' Objects
CreateSegmentation.data.frame | Create a 'Segmentation' Objects
CreateSegmentation.Segmentation | Create a 'Segmentation' Objects
CreateSegmentation.sf | Create a 'Segmentation' Objects
CreateSeuratObject | Create a 'Seurat' object
CreateSeuratObject.Assay | Create a 'Seurat' object
CreateSeuratObject.Assay5 | Create a 'Seurat' object
CreateSeuratObject.default | Create a 'Seurat' object
Crop | Crop Coordinates
Crop.FOV | Crop Coordinates

## -- D --

DefaultAssay | Default Assay
DefaultAssay.Assay | Default Assay
DefaultAssay.Assay5 | Default Assay
DefaultAssay.DimReduc | Default Assay
DefaultAssay.Graph | Default Assay
DefaultAssay.Seurat | Default Assay
DefaultAssay.SeuratCommand | Default Assay
DefaultAssay.SpatialImage | 'SpatialImage' methods
DefaultAssay<- | Default Assay
DefaultAssay<-.Assay | Default Assay
DefaultAssay<-.Assay5 | Default Assay
DefaultAssay<-.DimReduc | Default Assay
DefaultAssay<-.Graph | Default Assay
DefaultAssay<-.Seurat | Default Assay
DefaultAssay<-.SpatialImage | 'SpatialImage' methods
DefaultBoundary | Get, Set, and Query Segmentation Boundaries
DefaultBoundary.FOV | Get, Set, and Query Segmentation Boundaries
DefaultBoundary<- | Get, Set, and Query Segmentation Boundaries
DefaultBoundary<-.FOV | Get, Set, and Query Segmentation Boundaries
DefaultDimReduc | Set Default Dimensionality Reduction Set the default dimensionality reduction for a specific assay in a Seurat object.
DefaultDimReduc<- | Set Default Dimensionality Reduction Set the default dimensionality reduction for a specific assay in a Seurat object.
DefaultDimReduc<-.Seurat | Set Default Dimensionality Reduction Set the default dimensionality reduction for a specific assay in a Seurat object.
DefaultFOV | Get and Set the Default FOV
DefaultFOV.Seurat | Get and Set the Default FOV
DefaultFOV<- | Get and Set the Default FOV
DefaultFOV<-.Seurat | Get and Set the Default FOV
DefaultLayer | Default Layer
DefaultLayer.Assay | Default Layer
DefaultLayer.Assay5 | Default Layer
DefaultLayer<- | Default Layer
DefaultLayer<-.Assay5 | Default Layer
dim.Assay | Feature and Cell Numbers
dim.Assay5 | Feature and Cell Numbers
dim.DimReduc | Dimensional Reduction Meta-Information
dim.Neighbor | 'Neighbor' Methods
dim.Seurat | Feature and Cell Numbers
dim.SpatialImage | 'SpatialImage' methods
dimnames.Assay | Assay-Level Feature and Cell Names
dimnames.Assay5 | Assay-Level Feature and Cell Names
dimnames.DimReduc | Dimensional Reduction Meta-Information
dimnames.Seurat | Feature and Cell Names
dimnames<-.Assay | Assay-Level Feature and Cell Names
dimnames<-.Assay5 | Assay-Level Feature and Cell Names
dimnames<-.Seurat | Feature and Cell Names
DimReduc | The Dimensional Reduction Class
DimReduc-class | The Dimensional Reduction Class
DimReduc-validity | Dimensional Reduction Validity
Distances | Get the Neighbor nearest neighbors distance matrix
Distances.Neighbor | Get the Neighbor nearest neighbors distance matrix
droplevels.LogMap | Drop Unused Logical Map Values
droplevels.Seurat | Get, set, and manipulate an object's identity classes

## -- E --

Embeddings | Get Cell Embeddings
Embeddings.DimReduc | Get Cell Embeddings
Embeddings.Seurat | Get Cell Embeddings
EmptyMatrix | Empty Matrices

## -- F --

Features | Cell and Feature Names
Features.Assay5 | Cell and Feature Names
Features.FOV | 'FOV' Methods
Features.Molecules | 'Molecules' Methods
FetchData | Access cellular data
FetchData.DimReduc | Access cellular data
FetchData.FOV | 'FOV' Methods
FetchData.Seurat | Access cellular data
FilterObjects | Find Sub-objects of a Certain Class
FOV | The Field of View Object
FOV-class | The Field of View Object
FOV-methods | 'FOV' Methods
FOV-validity | FOV Validity

## -- G --

GetAssayData | Get and Set Assay Data
GetAssayData.Assay | Get and Set Assay Data
GetAssayData.Seurat | Get and Set Assay Data
GetImage | Get image data
GetImage.Seurat | Get image data
GetImage.SpatialImage | 'SpatialImage' methods
GetTissueCoordinates | Get tissue coordinates
GetTissueCoordinates.Centroids | 'Centroids' Methods
GetTissueCoordinates.FOV | Get tissue coordinates
GetTissueCoordinates.Molecules | 'Molecules' Methods
GetTissueCoordinates.Segmentation | 'Segmentation' Methods
GetTissueCoordinates.Seurat | Get tissue coordinates
GetTissueCoordinates.SpatialImage | 'SpatialImage' methods
Graph | The Graph Class
Graph-class | The Graph Class
Graphs | Query Specific Object Types

## -- H --

head.Assay | Feature-Level Meta Data
head.Assay5 | Feature-Level Meta Data
head.Seurat | Subobjects and Cell-Level Meta Data
HVFInfo | Highly Variable Features
HVFInfo.Assay | Highly Variable Features
HVFInfo.Assay5 | Highly Variable Features
HVFInfo.Seurat | Highly Variable Features

## -- I --

Idents | Get, set, and manipulate an object's identity classes
Idents.Seurat | Get, set, and manipulate an object's identity classes
Idents<- | Get, set, and manipulate an object's identity classes
Idents<-.Seurat | Get, set, and manipulate an object's identity classes
Images | Pull spatial image names
Index | Get Neighbor algorithm index
Index.Neighbor | Get Neighbor algorithm index
Index<- | Get Neighbor algorithm index
Index<-.Neighbor | Get Neighbor algorithm index
Indices | Get Neighbor nearest neighbor index matrices
Indices.Neighbor | Get Neighbor nearest neighbor index matrices
intersect.LogMap | Find Common Logical Map Values
is.finite.Centroids | 'Centroids' Methods
is.infinite.Centroids | 'Centroids' Methods
IsGlobal | Is an object global/persistent?
IsGlobal.default | Is an object global/persistent?
IsGlobal.DimReduc | Is an object global/persistent?
IsGlobal.SpatialImage | 'SpatialImage' methods
IsMatrixEmpty | Check if a matrix is empty
IsMatrixEmpty.default | Check if a matrix is empty
IsNamedList | Check List Names

## -- J --

JackStrawData | The JackStrawData Class
JackStrawData-class | The JackStrawData Class
JackStrawData-methods | 'JackStrawData' Methods
JoinLayers | Split and Join Layers Together
JoinLayers.Assay5 | Split and Join Layers Together
JoinLayers.Seurat | Split and Join Layers Together
JS | Get and set JackStraw information
JS.DimReduc | Get and set JackStraw information
JS.JackStrawData | Get and set JackStraw information
JS<- | Get and set JackStraw information
JS<-.DimReduc | Get and set JackStraw information
JS<-.JackStrawData | Get and set JackStraw information

## -- K --

Key | Get and set object keys
Key.Assay | Get and set object keys
Key.Assay5 | Get and set object keys
Key.DimReduc | Get and set object keys
Key.Seurat | Get and set object keys
Key.SpatialImage | 'SpatialImage' methods
Key<- | Get and set object keys
Key<-.Assay | Get and set object keys
Key<-.Assay5 | Get and set object keys
Key<-.DimReduc | Get and set object keys
Key<-.SpatialImage | 'SpatialImage' methods
Keys | Get and set object keys
Keys.FOV | 'FOV' Methods
Keys.Seurat | Get and set object keys

## -- L --

labels.LogMap | Find Observations by Value
LayerData | Query and Manipulate Assay Layers
LayerData.Assay | Query and Manipulate Assay Layers
LayerData.Assay5 | Query and Manipulate Assay Layers
LayerData.Seurat | Query and Manipulate Assay Layers
LayerData<- | Query and Manipulate Assay Layers
LayerData<-.Assay | Query and Manipulate Assay Layers
LayerData<-.Assay5 | Query and Manipulate Assay Layers
LayerData<-.Seurat | Query and Manipulate Assay Layers
Layers | Query and Manipulate Assay Layers
Layers.Assay | Query and Manipulate Assay Layers
Layers.Assay5 | Query and Manipulate Assay Layers
Layers.Seurat | Query and Manipulate Assay Layers
length.Centroids | 'Centroids' Methods
length.DimReduc | Dimensional Reduction Meta-Information
length.FOV | 'FOV' Methods
lengths.Centroids | 'Centroids' Methods
lengths.Segmentation | 'Segmentation' Methods
levels.Seurat | Get, set, and manipulate an object's identity classes
levels<-.Seurat | Get, set, and manipulate an object's identity classes
Loadings | Get and set feature loadings
Loadings.DimReduc | Get and set feature loadings
Loadings.Seurat | Get and set feature loadings
Loadings<- | Get and set feature loadings
Loadings<-.DimReduc | Get and set feature loadings
LoadSeuratRds | Save and Load 'Seurat' Objects from Rds files
LogMap | A Logical Map
LogMap-class | A Logical Map
LogMap-validity | Logical Map Validity
LogSeuratCommand | Log a command

## -- M --

merge | Merge Seurat Objects
merge.Assay | Merge Assays
merge.Assay5 | Merge Assays
merge.DimReduc | Merge Dimensional Reductions
merge.Seurat | Merge Seurat Objects
MergeSeurat | Merge Seurat Objects
Misc | Get and set miscellaneous data
Misc.Assay | Get and set miscellaneous data
Misc.Assay5 | Get and set miscellaneous data
Misc.DimReduc | Get and set miscellaneous data
Misc.Seurat | Get and set miscellaneous data
Misc<- | Get and set miscellaneous data
Misc<-.Assay | Get and set miscellaneous data
Misc<-.Assay5 | Get and set miscellaneous data
Misc<-.DimReduc | Get and set miscellaneous data
Misc<-.Seurat | Get and set miscellaneous data
Molecules | Get, Set, and Query Segmentation Boundaries
Molecules-class | The Spatial Molecules Class
Molecules-methods | 'Molecules' Methods
Molecules.FOV | Get, Set, and Query Segmentation Boundaries

## -- N --

names.DimReduc | Dimensional Reduction Meta-Information
names.FOV | 'FOV' Methods
names.Seurat | Subobject Names
Neighbor | The Neighbor class
Neighbor-class | The Neighbor class
Neighbor-methods | 'Neighbor' Methods
Neighbors | Query Specific Object Types

## -- O --

Overlay | Overlay 'Spatial' Objects Over One Another
Overlay-method | Overlay 'Spatial' Objects Over One Another

## -- P --

PackageCheck | Check the existence of a package
pbmc_small | A small example version of the PBMC dataset
print | Print Top Feature Loadings
print.DimReduc | Print Top Feature Loadings
Project | Get and set project information
Project.Seurat | Get and set project information
Project<- | Get and set project information
Project<-.Seurat | Get and set project information

## -- R --

Radius | Get the spot radius from an image
Radius.Centroids | 'Centroids' Methods
Radius.SpatialImage | 'SpatialImage' methods
RandomName | Generate a random name
Reductions | Query Specific Object Types
remove-object | Remove Subobjects and Cell-Level Meta Data
remove-objects | Remove Subobjects and Cell-Level Meta Data
RenameAssays | Rename assays in a 'Seurat' object
RenameCells | Rename cells
RenameCells.Assay | Rename cells
RenameCells.Assay5 | Rename cells
RenameCells.Centroids | 'Centroids' Methods
RenameCells.DimReduc | Rename cells
RenameCells.FOV | 'FOV' Methods
RenameCells.Neighbor | Rename cells
RenameCells.Segmentation | 'Segmentation' Methods
RenameCells.Seurat | Rename cells
RenameCells.SpatialImage | 'SpatialImage' methods
RenameIdent | Get, set, and manipulate an object's identity classes
RenameIdents | Get, set, and manipulate an object's identity classes
RenameIdents.Seurat | Get, set, and manipulate an object's identity classes
ReorderIdent | Get, set, and manipulate an object's identity classes
ReorderIdent.Seurat | Get, set, and manipulate an object's identity classes
RowMergeSparseMatrices | Merge Sparse Matrices by Row

## -- S --

SaveSeuratRds | Save and Load 'Seurat' Objects from Rds files
Segmentation-class | The 'Segmentation' Class
Segmentation-methods | 'Segmentation' Methods
Segmentation-validity | Segmentation Validity
set-if-null | Set If or If Not 'NULL'
SetAssayData | Get and Set Assay Data
SetAssayData.Assay | Get and Set Assay Data
SetAssayData.Seurat | Get and Set Assay Data
SetDimReduction | Create a DimReduc object
SetIdent | Get, set, and manipulate an object's identity classes
SetIdent.Seurat | Get, set, and manipulate an object's identity classes
Seurat | The Seurat Class
Seurat-class | The Seurat Class
Seurat-validity | Seurat Object Validity
SeuratAccess | Add in metadata associated with either cells or features.
SeuratCommand | The 'SeuratCommand' Class
SeuratCommand-class | The 'SeuratCommand' Class
SeuratObject | SeuratObject: Data Structures for Single Cell Data
show-method | 'Centroids' Methods
show-method | 'FOV' Methods
show-method | 'JackStrawData' Methods
show-method | 'Molecules' Methods
show-method | 'Neighbor' Methods
show-method | 'Segmentation' Methods
show-method | 'SpatialImage' methods
show-method | 'LogMap' Object Overview
Simplify | Simplify Geometry
Simplify.Spatial | Simplify Geometry
SpatialImage | The SpatialImage class
SpatialImage-class | The SpatialImage class
SpatialImage-methods | 'SpatialImage' methods
SpatiallyVariableFeatures | Highly Variable Features
SpatiallyVariableFeatures.Assay | Highly Variable Features
SpatiallyVariableFeatures.Assay5 | Highly Variable Features
SpatiallyVariableFeatures.Seurat | Highly Variable Features
split.Assay | Split an Assay
split.Assay5 | Split an Assay
StashIdent | Get, set, and manipulate an object's identity classes
StashIdent.Seurat | Get, set, and manipulate an object's identity classes
Stdev | Get the standard deviations for an object
Stdev.DimReduc | Get the standard deviations for an object
Stdev.Seurat | Get the standard deviations for an object
StitchMatrix | Stitch Matrices Together
subset | Subset 'Seurat' Objects
subset.Assay | Subset an Assay
subset.Assay5 | Subset an Assay
subset.Centroids | 'Centroids' Methods
subset.DimReduc | Subset a Dimensional Reduction
subset.FOV | 'FOV' Methods
subset.Molecules | 'Molecules' Methods
subset.Segmentation | 'Segmentation' Methods
subset.Seurat | Subset 'Seurat' Objects
subset.SpatialImage | 'SpatialImage' methods
SVFInfo | Highly Variable Features
SVFInfo.Assay | Highly Variable Features
SVFInfo.Assay5 | Highly Variable Features
SVFInfo.Seurat | Highly Variable Features
SVFInfo.StdAssay | Highly Variable Features

## -- T --

tail.Assay | Feature-Level Meta Data
tail.Assay5 | Feature-Level Meta Data
tail.Seurat | Subobjects and Cell-Level Meta Data
Theta | Get the offset angle
Theta.Centroids | 'Centroids' Methods
Tool | Get and Set Additional Tool Data
Tool.Seurat | Get and Set Additional Tool Data
Tool<- | Get and Set Additional Tool Data
Tool<-.Seurat | Get and Set Additional Tool Data
Tools | Get and Set Additional Tool Data

## -- U --

UpdateSeuratObject | Update old Seurat object to accommodate new features
UpdateSlots | Update slots in an object

## -- V --

VariableFeatures | Highly Variable Features
VariableFeatures.Assay | Highly Variable Features
VariableFeatures.Assay5 | Highly Variable Features
VariableFeatures.Seurat | Highly Variable Features
VariableFeatures<- | Highly Variable Features
VariableFeatures<-.Assay | Highly Variable Features
VariableFeatures<-.Seurat | Highly Variable Features
Version | Get Version Information
Version.Seurat | Get Version Information

## -- W --

WhichCells | Identify cells matching certain criteria
WhichCells.Assay | Identify cells matching certain criteria
WhichCells.Seurat | Identify cells matching certain criteria

## -- misc --

$.Assay | Layer Data
$.Assay5 | Layer Data
$.FOV | 'FOV' Methods
$.JackStrawData | 'JackStrawData' Methods
$.Seurat | Cell-Level Meta Data
$.SeuratCommand | Command Log Parameter Access
$<-.Assay | Layer Data
$<-.Assay5 | Layer Data
$<-.Seurat | Cell-Level Meta Data
%iff% | Set If or If Not 'NULL'
%||% | Set If or If Not 'NULL'
.DollarNames.JackStrawData | 'JackStrawData' Methods
.DollarNames.SeuratCommand | Dollar-sign Autocompletion
[-method | 'Centroids' Methods
[-method | 'Segmentation' Methods
[.Assay | Layer Data
[.Assay5 | Layer Data
[.DimReduc | Get Feature Loadings
[.FOV | 'FOV' Methods
[.Seurat | Subset 'Seurat' Objects
[.SeuratCommand | Command Log Data Access
[.SpatialImage | 'SpatialImage' methods
[<--method | Layer Data
[<--method | Layer Data
[[-method | A Logical Map
[[.Assay | Feature-Level Meta Data
[[.Assay5 | Feature-Level Meta Data
[[.DimReduc | Get Cell Embeddings
[[.FOV | 'FOV' Methods
[[.Seurat | Subobjects and Cell-Level Meta Data
[[<-,Seurat | Add Subobjects
[[<-,Seurat,NULL | Remove Subobjects and Cell-Level Meta Data
[[<--method | 'FOV' Methods
[[<--method | A Logical Map
[[<--method | 'Segmentation' Methods
[[<--method | Cell-Level Meta Data
[[<--method | Feature-Level Meta Data
[[<--method | Feature-Level Meta Data
[[<--method | Remove Subobjects and Cell-Level Meta Data
[[<--method | Add Subobjects
[[<-.Seurat | Add Subobjects
\S4method{[[<-}{Seurat,character,missing,Assay} | Add Subobjects
\S4method{[[<-}{Seurat,character,missing,NULL} | Remove Subobjects and Cell-Level Meta Data