An S4 class that contains all elements needed for CA.

Class to store biclustering clustering results.

Slots

cell_clusters

factors. The assigned cell clusters with cell names in the names attribute.

gene_clusters

factors. The assigned gene clusters with gene names in the names attribute.

SNN

sparse shared nearest neighbours matrix. Values indicate the jaccard similarity.

parameters

List of used parameters and function name with which results were generated.

eigen

matrix, Slot for storing eigenvectors from spectral clustering

cell_prob

matrix. Matrix that stores the probabilities that a cell belongs to a cluster. Only filled when running spectral clustering with GMM.

gene_prob

matrix. Matrix that stores the probabilities that a gene belongs to a cluster. Only filled when running spectral clustering with GMM.

cell_idxs

integer. Indices of the cells in the SNN adjacency matrix.

gene_idxs

integer. Indices of the genes in the SNN adjacency matrix.

bimap

data.frame. Data frame storing the biMAP coordinates (x, y) and the type (cell or gene) as well as the assigned clusters.