R: The Seurat Class

seurat-class {SeuratObject} | R Documentation

## The Seurat Class

### Description

The Seurat object is the center of each single cell analysis. It stores all information associated with the dataset, including data, annotations, analyses, etc. All that is needed to construct a Seurat object is an expression matrix (rows are genes, columns are cells), which should be log-scale

### Usage

    ## S4 method for signature 'seurat'
    show(object)

### Arguments

`object` | A `Seurat` object

### Details

Each Seurat object has a number of slots which store information. Key slots to access are listed below.

### Slots

`raw.data`

  The raw project data

`data`

  The normalized expression matrix (log-scale)

`scale.data`

  scaled (default is z-scoring each gene) expression matrix; used for dimensional reduction and heatmap visualization

`var.genes`

  Vector of genes exhibiting high variance across single cells

`is.expr`

  Expression threshold to determine if a gene is expressed (0 by default)

`ident`

  THe 'identity class' for each cell

`meta.data`

  Contains meta-information about each cell, starting with number of genes detected (nFeature) and the original identity class (orig.ident); more information is added using `AddMetaData`

`project.name`

  Name of the project (for record keeping)

`dr`

  List of stored dimensional reductions; named by technique

`assay`

  List of additional assays for multimodal analysis; named by technique

`hvg.info`

  The output of the mean/variability analysis for all genes

`imputed`

  Matrix of imputed gene scores

`cell.names`

  Names of all single cells (column names of the expression matrix)

`cluster.tree`

  List where the first element is a phylo object containing the phylogenetic tree relating different identity classes

`snn`

  Spare matrix object representation of the SNN graph

`calc.params`

  Named list to store all calculation-related parameter choices

`kmeans`

  Stores output of gene-based clustering from `DoKMeans`

`spatial`

  Stores internal data and calculations for spatial mapping of single cells

`misc`

  Miscellaneous spot to store any data alongside the object (for example, gene lists)

`version`

  Version of package used in object creation

[Package SeuratObject version 4.0.3 Index]