Data Structures for Single Cell Data

Documentation for package ‘SeuratObject’ version 5.0.2

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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
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	Find the default 'DimReduc'
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	'FOV' Methods
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
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.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.Seurat	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<-.Assay5	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	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