R/class_definitions.R

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

#' The domino Class
#' 
#' 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.
#' 
#' @slot db_info List of data sets from lr database.
#' @slot counts Raw count gene expression data
#' @slot z_scores Matrix of z-scored expression data with cells as columns
#' @slot clusters Named factor with cluster identity of each cell
#' @slot features Matrix of features to correlate receptor-ligand expression with. Cells are columns and features are rows.
#' @slot df List containing transcriptional targets by transcription factor.
#' @slot cor Correlation matrix of receptor expression to features.
#' @slot linkages List of lists containing info linking cluster->tf->rec->lig
#' @slot clust_de Data frame containing differential expression results for features by cluster.
#' @slot misc List of miscellaneous info pertaining to run parameters etc.
#' @slot cl_signaling_matrices Incoming signaling matrix for each cluster
#' @slot signaling Signaling matrix between all clusters.
#' 
#' @name domino-class
#' @rdname domino-class
#' @exportClass domino
#' 
domino <- setClass(
    Class = 'domino',
    slots = c(
        db_info = 'list',
        z_scores = 'matrix',
        counts = 'AnyMatrix',
        clusters = 'factor',
        features = 'matrix',
        cor = 'matrix',
        linkages = 'list',
        clust_de = 'matrix',
        misc = 'list',
        cl_signaling_matrices = 'list',
        signaling = 'matrix'
    )
)

print.domino = function(dom){
    cat('A Domino object of', length(dom@clusters), 'cells.\n')
}