Data Structures for Single Cell Data
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Documentation for package ‘SeuratObject’ version 4.1.4
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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.Seurat | Add in metadata associated with either cells or features. |
| AddSamples | Seurat Methods |
| aggregate | Aggregate Molecules into an Expression Matrix |
| aggregate.FOV | Aggregate Molecules into an Expression Matrix |
| aggregate.Molecules | Aggregate Molecules into an Expression Matrix |
| 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 | 'SeuratCommand' Methods |
| as.logical.JackStrawData | 'JackStrawData' Methods |
| 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-methods | 'Assay' Methods |
| AssayData | Get and Set Assay Data |
| Assays | 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 --
| Cells | 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 |
| colMeans-method | 'Assay' Methods |
| colMeans-method | Seurat Methods |
| colSums-method | 'Assay' Methods |
| colSums-method | Seurat Methods |
| Command | Get SeuratCommands |
| Command.Seurat | Get SeuratCommands |
| coordinates-method | 'Segmentation' Methods |
| 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.default | Create a 'Seurat' object |
| Crop | Crop Coordinates |
| Crop.FOV | Crop Coordinates |
-- D --
| DefaultAssay | Default Assay |
| DefaultAssay.Assay | 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<-.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 |
| dim.Assay | 'Assay' Methods |
| dim.DimReduc | 'DimReduc' Methods |
| dim.Neighbor | 'Neighbor' Methods |
| dim.Seurat | Seurat Methods |
| dim.SpatialImage | 'SpatialImage' methods |
| dimnames.Assay | 'Assay' Methods |
| dimnames.DimReduc | 'DimReduc' Methods |
| dimnames.Seurat | Seurat Methods |
| DimReduc | The Dimensional Reduction Class |
| DimReduc-class | The Dimensional Reduction Class |
| DimReduc-methods | 'DimReduc' Methods |
| Distances | Get the Neighbor nearest neighbors distance matrix |
| Distances.Neighbor | Get the Neighbor nearest neighbors distance matrix |
| 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.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 |
-- 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 | 'Assay' Methods |
| head.Seurat | Seurat Methods |
| HVFInfo | Highly Variable Features |
| HVFInfo.Assay | 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 |
| 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 |
| IsNamedList | Check List Names |
| IsS4List | S4/List Conversion |
-- J --
| JackStrawData | The JackStrawData Class |
| JackStrawData-class | The JackStrawData Class |
| JackStrawData-methods | 'JackStrawData' Methods |
| 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.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<-.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 --
| length.Centroids | 'Centroids' Methods |
| length.DimReduc | 'DimReduc' Methods |
| 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 |
| ListToS4 | S4/List Conversion |
| 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 |
| LogMap | A Logical Map |
| LogMap-class | A Logical Map |
| LogSeuratCommand | Log a command |
-- M --
| MatchCells | Match Cells |
| MatchCells.character | Match Cells |
| MatchCells.NULL | Match Cells |
| MatchCells.numeric | Match Cells |
| merge | Seurat Methods |
| merge.Assay | 'Assay' Methods |
| merge.DimReduc | 'DimReduc' Methods |
| merge.Seurat | Seurat Methods |
| MergeSeurat | Seurat Methods |
| Misc | Get and set miscellaneous data |
| Misc.Assay | 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<-.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 | 'DimReduc' Methods |
| names.FOV | 'FOV' Methods |
| names.Seurat | Seurat Methods |
| 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 |
| 'DimReduc' Methods | |
| print.DimReduc | 'DimReduc' Methods |
| 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 |
| RenameAssays | Rename assays in a 'Seurat' object |
| RenameCells | Rename cells |
| RenameCells.Assay | 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 |
| rowMeans-method | 'Assay' Methods |
| rowMeans-method | Seurat Methods |
| RowMergeSparseMatrices | Merge Sparse Matrices by Row |
| rowSums-method | 'Assay' Methods |
| rowSums-method | Seurat Methods |
-- S --
| s4list | S4/List Conversion |
| S4ToList | S4/List Conversion |
| S4ToList.default | S4/List Conversion |
| S4ToList.list | S4/List Conversion |
| Segmentation-class | The 'Segmentation' Class |
| Segmentation-methods | 'Segmentation' Methods |
| set-if-na | Set if 'NA' |
| 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-methods | Seurat Methods |
| SeuratAccess | Add in metadata associated with either cells or features. |
| SeuratCommand | The SeuratCommand Class |
| SeuratCommand-class | The SeuratCommand Class |
| SeuratCommand-methods | 'SeuratCommand' Methods |
| SeuratObject | SeuratObject: Data Structures for Single Cell Data |
| show-method | 'Assay' Methods |
| show-method | 'Centroids' Methods |
| show-method | 'DimReduc' Methods |
| show-method | 'FOV' Methods |
| show-method | 'JackStrawData' Methods |
| show-method | A Logical Map |
| show-method | 'Molecules' Methods |
| show-method | 'Neighbor' Methods |
| show-method | 'Segmentation' Methods |
| show-method | Seurat Methods |
| show-method | 'SeuratCommand' Methods |
| show-method | 'SpatialImage' methods |
| 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 |
| 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 |
| subset | Seurat Methods |
| subset.Assay | 'Assay' Methods |
| subset.Centroids | 'Centroids' Methods |
| subset.DimReduc | 'DimReduc' Methods |
| subset.FOV | 'FOV' Methods |
| subset.Molecules | 'Molecules' Methods |
| subset.Segmentation | 'Segmentation' Methods |
| subset.Seurat | Seurat Methods |
| subset.SpatialImage | 'SpatialImage' methods |
| SVFInfo | Highly Variable Features |
| SVFInfo.Assay | Highly Variable Features |
| SVFInfo.Seurat | Highly Variable Features |
-- T --
| tail.Assay | 'Assay' Methods |
| tail.Seurat | Seurat Methods |
| 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.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 --
| $.FOV | 'FOV' Methods |
| $.JackStrawData | 'JackStrawData' Methods |
| $.Seurat | Seurat Methods |
| $.SeuratCommand | 'SeuratCommand' Methods |
| $<-.Seurat | Seurat Methods |
| %!NA% | Set if 'NA' |
| %!na% | Set if 'NA' |
| %NA% | Set if 'NA' |
| %na% | Set if 'NA' |
| .DollarNames.JackStrawData | 'JackStrawData' Methods |
| .DollarNames.Seurat | Seurat Methods |
| .DollarNames.SeuratCommand | 'SeuratCommand' Methods |
| [-method | 'Centroids' Methods |
| [-method | 'Segmentation' Methods |
| [.Assay | 'Assay' Methods |
| [.DimReduc | 'DimReduc' Methods |
| [.FOV | 'FOV' Methods |
| [.Seurat | Seurat Methods |
| [.SeuratCommand | 'SeuratCommand' Methods |
| [.SpatialImage | 'SpatialImage' methods |
| [[-method | A Logical Map |
| [[.Assay | 'Assay' Methods |
| [[.DimReduc | 'DimReduc' Methods |
| [[.FOV | 'FOV' Methods |
| [[.Seurat | Seurat Methods |
| [[<--method | 'Assay' Methods |
| [[<--method | 'FOV' Methods |
| [[<--method | A Logical Map |
| [[<--method | Seurat Methods |