Dimreduc object

Author: hsln

August undefined, 2024

Webdim (DimReduc): The number of cells and dimensions for a DimReduc dimnames (DimReduc): The cell and dimension names for a DimReduc object length (DimReduc): The number of dimensions for a DimReduc object merge (DimReduc): Merge two or more DimReduc objects together names (DimReduc): The dimension names for a … WebDescription Change the cell names in all the different parts of an object. Can be useful before combining multiple objects. Usage RenameCells (object, ...) # S3 method for Assay RenameCells (object, new.names = NULL, ...) # S3 method for DimReduc RenameCells (object, new.names = NULL, ...)

Visualize

WebMar 27, 2024 · In Seurat v3.0, storing and interacting with dimensional reduction information has been generalized and formalized into the DimReduc object. Each … Web# S3 method for DimReduc Key(object, ...) <- value # S3 method for Seurat Key(object, ...) # S3 method for Seurat Keys(object, ...) Arguments object An object ... Arguments … organic cleaning wipes

Run UMAP — RunUMAP • Seurat - Satija Lab

Webobject. An object... Arguments passed to other methods. new.names. vector of new cell names. old.names. vector of old cell names. add.cell.id. prefix to add cell names. for.merge. Only rename slots needed for merging Seurat objects. Currently only renames the raw.data and meta.data slots. WebNov 10, 2024 · dim(DimReduc): The number of cells and dimensions for a DimReduc. dimnames(DimReduc): The cell and dimension names for a DimReduc object … how to use cricut deep point blade

Run UMAP — RunUMAP • Seurat - Satija Lab

WebDimReduc object that contains the umap model return.model whether UMAP will return the uwot model umap.method UMAP implementation to run. Can be uwot: Runs umap via … WebNov 10, 2024 · A DimReduc object Examples data <- GetAssayData (pbmc_small [ ["RNA"]], slot = "scale.data") pcs <- prcomp (x = data) pca.dr <- CreateDimReducObject ( … organic clean kelpWebcustom DimReduc: User provided DimReduc object computed on the query cells l2.norm Perform L2 normalization on the cell embeddings after dimensional reduction dims Set of dimensions to use in the anchor weighting procedure. If NULL, the same dimensions that were used to find anchors will be used for weighting. k.weight organic cleankelp

"Accessing data from an DimReduc object is done in several ways. Feature loadings is accessed with the Loadings function. Pulling feature loadings can … See more Summary information about DimReduc objects can be had quickly and easily using standard R functions. The number of cell embeddings and feature loadings can … See more Methods for the DimReducclass can be found with the following: 1. [ 2. [<- 3. [[ 4. [[<- 5. DefaultAssay 6. DefaultAssay<- 7. dim 8. dimnames 9. Embeddings 10. … See more " - Dimreduc object

Dimreduc object

WebJun 24, 2024 · Explore the new dimensional reduction structure In Seurat v3.0, storing and interacting with dimensional reduction information has been generalized and formalized into the DimReduc object. Each dimensional reduction procedure is stored as a DimReduc object in the object@reductions slot as an element of a named list. WebCreate a DimReduc object. Source: R/dimreduc.R. Create a DimReduc object. CreateDimReducObject( embeddings = new(Class = "matrix"), loadings = new(Class …

Did you know?

Webdim (Seurat): Number of cells and features for the active assay dimnames (Seurat): The cell and feature names for the active assay head (Seurat): Get the first rows of cell-level metadata merge (Seurat): Merge two or more Seurat objects together names (Seurat): Common associated objects subset (Seurat): Subset a Seurat object WebThe Dimensional Reduction Class. Source: R/dimreduc.R. The DimReduc object stores a dimensionality reduction taken out in Seurat; each DimReduc consists of a cell …

WebCreate 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. WebOct 28, 2024 · I had to keep recreating the sce object with sce = SingleCellExperiment(list(counts=data_mat)) every time I wanted to do something with sce (e.g. emptyDrops and scDblFinder) because when it was freshly created, it had "counts" as the assay, however if I saved this sce object to the environment and called it again in the …

WebNov 19, 2024 · FeaturePlot ( object, features, dims = c (1, 2), cells = NULL, cols = if (blend) { c ("lightgrey", "#ff0000", "#00ff00") } else { c ("lightgrey", "blue") }, pt.size = NULL, order = FALSE, min.cutoff = NA, max.cutoff = NA, reduction = NULL, split.by = NULL, keep.scale = "feature", shape.by = NULL, slot = "data", blend = FALSE, blend.threshold = … WebAug 27, 2024 · DimReduc objects represent transformations of the data contained within the Assay object (s) via various dimensional reduction techniques such as PCA. For class-specific details, including more in depth description of the slots, please see the wiki sections for …

WebRun this code # NOT RUN { # Get the embeddings directly from a DimReduc object Embeddings (object = pbmc_small [ ["pca"]]) [1:5, 1:5] # Get the embeddings from a specific DimReduc in a Seurat object Embeddings (object = pbmc_small, reduction = "pca") [1:5, 1:5] # } Run the code above in your browser using DataCamp Workspace

WebThe DimReduc object stores a dimensionality reduction taken out in Seurat; each DimReduc consists of a cell embeddings matrix, a feature loadings matrix, and a projected feature loadings matrix. RDocumentation. Search all … how to use cricut appWebSet 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 ... how to use cricut explore air 2 for dummiesWebDimReduc object that contains the umap model return.model whether UMAP will return the uwot model umap.method UMAP implementation to run. Can be uwot: Runs umap via … how to use cricut foil iron on videoWebA column name from a DimReduc object corresponding to the cell embedding values (e.g. the PC 1 scores - "PC_1") dims Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions cells Vector of cells to plot (default is all cells) cols The two colors to form the gradient over. organic clean protein shake reviewWebx, object: A DimReduc object. i: For [: feature names or indices; for [[: cell names or indices. j: Dimensions to pull for. drop: See drop. Arguments passed to other methods. y: … how to use cricut foil kitWebSeuratObject(version 4.1.3) DimReduc-class: The Dimensional Reduction Class. Description. The DimReduc object stores a dimensionality reduction taken out in … how to use cricut explore air 2 for vinylWebCreate a DimReduc object Usage CreateDimReducObject( embeddings = new(Class = "matrix"), loadings = new(Class = "matrix"), projected = new(Class = "matrix"), assay = … organic cleaning services