domino-class: The domino Class
In Chris-Cherry/domino: Receptor Ligand Analysis for Single Cell RNA Seq

domino-class

R Documentation

The domino Class

Description

The domino class contains all information necessary to calculate receptor ligand signaling. It contains z scored expression, cluster, feature values, and formatted receptor ligand databases as well as all calculated intermediates.

Slots

db_info: List of data sets from lr database.
counts: Raw count gene expression data
z_scores: Matrix of z-scored expression data with cells as columns
clusters: Named factor with cluster identity of each cell
features: Matrix of features to correlate receptor-ligand expression with. Cells are columns and features are rows.
df: List containing transcriptional targets by transcription factor.
cor: Correlation matrix of receptor expression to features.
linkages: List of lists containing info linking cluster->tf->rec->lig
clust_de: Data frame containing differential expression results for features by cluster.
misc: List of miscellaneous info pertaining to run parameters etc.
cl_signaling_matrices: Incoming signaling matrix for each cluster
signaling: Signaling matrix between all clusters.