Data Structures for Single Cell Data


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Documentation for package ‘SeuratObject’ version 5.0.1

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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
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

-- 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