R/AllGenerics.R

In scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

#' @name norm_exprs
#' @aliases norm_exprs
#' @export
#' @docType methods
#' @return a matrix of normalised expression data
#' @rdname accessors
setGeneric("norm_exprs", function(object) standardGeneric("norm_exprs"))

#' @name norm_exprs<-
#' @aliases norm_exprs<-
#' @export
#' @docType methods
#' @rdname accessors
setGeneric("norm_exprs<-", function(object, value) standardGeneric("norm_exprs<-"))

#' @name stand_exprs
#' @aliases stand_exprs
#' @export
#' @docType methods
#' @return a matrix of standardised expressiond data
#' @rdname accessors
setGeneric("stand_exprs", function(object) standardGeneric("stand_exprs"))

#' @name stand_exprs<-
#' @aliases stand_exprs<-
#' @export
#' @docType methods
#' @rdname accessors
setGeneric("stand_exprs<-", function(object, value) standardGeneric("stand_exprs<-"))

#' @name bootstraps
#' @export
#' @docType methods
#' @rdname bootstraps
setGeneric("bootstraps", function(object) standardGeneric("bootstraps"))

#' @name bootstraps<-
#' @export
#' @docType methods
#' @rdname bootstraps
setGeneric("bootstraps<-", function(object, value) standardGeneric("bootstraps<-"))

#' @name fpkm
#' @aliases  fpkm
#' @export
#' @docType methods
#' @return a matrix of FPKM values
#' @rdname accessors
setGeneric("fpkm", function(object) standardGeneric("fpkm"))

#' @name fpkm<-
#' @aliases  fpkm<-
#' @export
#' @docType methods
#' @rdname accessors
setGeneric("fpkm<-", function(object, value) standardGeneric("fpkm<-"))

####################################
# Dimensionality reduction generics.

#' @export
#' @rdname runPCA
setGeneric("calculatePCA", function(x, ...) standardGeneric("calculatePCA"))

#' @export
#' @rdname runTSNE
setGeneric("calculateTSNE", function(x, ...) standardGeneric("calculateTSNE"))

#' @export
#' @rdname runUMAP
setGeneric("calculateUMAP", function(x, ...) standardGeneric("calculateUMAP"))

#' @export
#' @rdname runMDS
setGeneric("calculateMDS", function(x, ...) standardGeneric("calculateMDS"))

#' @export
#' @rdname runNMF
setGeneric("calculateNMF", function(x, ...) standardGeneric("calculateNMF"))

#' @export
#' @rdname runDiffusionMap
setGeneric("calculateDiffusionMap", function(x, ...) standardGeneric("calculateDiffusionMap"))