The Seurat object is the center of each single cell analysis. It stores all information associated with the dataset, including data, annotations, analyes, 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
raw.data:"ANY", The raw project data
data:"ANY", The normalized expression matrix (log-scale)
scale.data:"ANY", The scaled (default is z-scoring
each gene) expression matrix. Used for dimensional reduction and heatmap visualization
var.genes:"vector", Vector of genes exhibiting high variance across single cells
is.expr:"numeric", Expression threshold to determine if a gene is expressed (0 by default)
ident:"factor", The 'identity class' for each single cell
meta.data:"data.frame", Contains information about metadata each cell, starting with # of genes detected (nGene)
the original identity class (orig.ident), user-provided information (through AddMetaData), etc.
project.name:"character", Name of the project (for record keeping)
dr:"list", List of stored dimensional reductions. Named by technique
assay:"list", List of additional assays for multimodal analysis. Named by technique
hvg.info:"data.frame", The output of the mean/variability analysis for all genes
imputed:"data.frame", Matrix of imputed gene scores
cell.names:"vector", Names of all single cells (column names of the expression matrix)
cluster.tree:"list", List where the first element is a phylo object containing the
phylogenetic tree relating different identity classes
snn:"dgCMatrix", Sparse matrix object representation of the SNN graph
calc.params:"list", Named list to store all calculation related parameters choices
kmeans:"ANY", Stores output of gene-based clustering from DoKMeans
spatial:"ANY",Stores internal data and calculations for spatial mapping of single cells
misc:"ANY", Miscellaneous spot to store any data alongisde the object (for example, gene lists)
version:"ANY", Version of package used in object creation
Each Seurat object has a number of slots which store information. Key slots to access are listed below.