Description
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
Slots
data:"data.frame", The expression matrix (log-scale) scale.data:"data.frame", The scaled (after z-scoring
each gene) expression matrix. Used for PCA, ICA, and heatmap plottingvar.genes:"vector", Variable genes across single cells is.expr:"numeric", Expression threshold to determine if a gene is expressed ident:"vector", The 'identity class' for each single cell data.info:"data.frame", Contains information about 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) pca.x:"data.frame", Gene projection scores for the PCA analysis pca.x.full:"data.frame", Gene projection scores for the projected PCA (contains all genes) pca.rot:"data.frame", The rotation matrix (eigenvectors) of the PCA ica.x:"data.frame", Gene projection scores for ICA ica.rot:"data.frame", The estimated source matrix from ICA tsne.rot:"data.frame", Cell coordinates on the t-SNE map mean.var:"data.frame", The output of the mean/variability analysis for all genes imputed:"data.frame", Matrix of imputed gene scores final.prob:"data.frame", For spatial inference, posterior probability of each cell mapping to each bin insitu.matrix:"data.frame", For spatial inference, the discretized spatial reference map 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
Details
Each Seurat object has a number of slots which store information. Key slots to access
are listed below.