R/AllGenerics.R

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

### defining all generic methods

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

#' @name get_exprs
#' @export
#' @docType methods
#' @return a matrix of expression values
#' @rdname get_exprs
setGeneric("get_exprs", function(object, exprs_values, ...) {
    standardGeneric("get_exprs")})

#' @name set_exprs<-
#' @export
#' @docType methods
#' @return NULL, but adds expression data to the SCESet object
#' @rdname set_exprs
setGeneric("set_exprs<-", function(object, name, value) {
    standardGeneric("set_exprs<-")})

#' @name is_exprs
#' @export
#' @docType methods
#' @return a logical matrix indicating if observations are "expressed" or not
#' @rdname is_exprs
setGeneric("is_exprs", function(object) {standardGeneric("is_exprs")})

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


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

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

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

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


#' @name tpm
#' @export
#' @docType methods
#' @return a matrix of transcripts-per-million data
#' @rdname tpm
setGeneric("tpm", function(object) {standardGeneric("tpm")})

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

#' @name cpm
#' @export
#' @docType methods
#' @return a matrix of counts-per-million values
#' @rdname cpm
setGeneric("cpm", function(object) {standardGeneric("cpm")})

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

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

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

#' @name norm_counts
#' @export
#' @docType methods
#' @return a matrix of normalised count data
#' @rdname norm_counts
setGeneric("norm_counts", function(object) {standardGeneric("norm_counts")})

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

#' @name norm_tpm
#' @export
#' @docType methods
#' @return a matrix of normalised transcripts-per-million data
#' @rdname norm_tpm
setGeneric("norm_tpm", function(object) {standardGeneric("norm_tpm")})

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

#' @name norm_cpm
#' @export
#' @docType methods
#' @return a matrix of normalised counts-per-million data
#' @rdname norm_cpm
setGeneric("norm_cpm", function(object) {standardGeneric("norm_cpm")})

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

#' @name norm_fpkm
#' @export
#' @docType methods
#' @return a matrix of normalised FPKM data
#' @rdname norm_fpkm
setGeneric("norm_fpkm", function(object) {standardGeneric("norm_fpkm")})

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

#' @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 cellPairwiseDistances
#' @export
#' @docType methods
#' @rdname cellPairwiseDistances
setGeneric("cellPairwiseDistances", function(object) {
    standardGeneric("cellPairwiseDistances")
    })

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


#' @name cellDist
#' @export
#' @docType methods
#' @rdname cellPairwiseDistances
setGeneric("cellDist", function(object) {
    standardGeneric("cellDist")
})

#' @name cellDist<-
#' @export
#' @docType methods
#' @rdname cellPairwiseDistances
setGeneric("cellDist<-", function(object, value) {
    standardGeneric("cellDist<-")
})


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

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


#' @name featDist
#' @export
#' @docType methods
#' @rdname featurePairwiseDistances
setGeneric("featDist", function(object) {
    standardGeneric("featDist")
})

#' @name featDist<-
#' @export
#' @docType methods
#' @rdname featurePairwiseDistances
setGeneric("featDist<-", function(object, value) {
    standardGeneric("featDist<-")
})

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

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


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

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


#' @name redDim
#' @export
#' @docType methods
#' @rdname reducedDimension
setGeneric("redDim", function(object) {
    standardGeneric("redDim")
})

#' @name redDim<-
#' @export
#' @docType methods
#' @rdname reducedDimension
setGeneric("redDim<-", function(object, value) {
    standardGeneric("redDim<-")
})

#' @name plotReducedDim
#' @export
#' @docType methods
#' @rdname plotReducedDim
setGeneric("plotReducedDim", function(object, ...) {
    standardGeneric("plotReducedDim")
})

#' @name plotExpression
#' @export
#' @docType methods
#' @rdname plotExpression
setGeneric("plotExpression", function(object, ...) {
    standardGeneric("plotExpression")
})


# #' @name plotPCA
# #' @export
# #' @docType methods
# #' @rdname plotPCA
# if ( !isGeneric("plotPCA") ) {
#     ## plotPCA is a generic in BiocGenerics_0.14.0 in R 3.2.0 - for earlier
#     ## versions need to manually add it as a generic
#     setGeneric("plotPCA", function(object, ...) {
#         standardGeneric("plotPCA")
#     })
# }

#' @name plotTSNE
#' @export
#' @docType methods
#' @rdname plotTSNE
setGeneric("plotTSNE", function(object, ...) {
    standardGeneric("plotTSNE")
})

#' @name plotDiffusionMap
#' @export
#' @docType methods
#' @rdname plotDiffusionMap
setGeneric("plotDiffusionMap", function(object, ...) {
    standardGeneric("plotDiffusionMap")
})

#' @name plotMDS
#' @export
#' @docType methods
#' @rdname plotMDS
setGeneric("plotMDS", function(object, ...) {
    standardGeneric("plotMDS")
})

## dplyr-style verb genetics

#' @name mutate
#' @rdname mutate
#' @docType methods
#' @export
setGeneric("mutate", function(object, ...) {
  standardGeneric("mutate")})

#' @name rename
#' @rdname rename
#' @docType methods
#' @export
setGeneric("rename", function(object, ...) {
  standardGeneric("rename")})

#' @name filter
#' @rdname filter
#' @docType methods
#' @export
setGeneric("filter", function(object, ...) {
  standardGeneric("filter")})

#' @name arrange
#' @rdname arrange
#' @docType methods
#' @export
setGeneric("arrange", function(object, ...) {
  standardGeneric("arrange")})

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

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

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

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

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

#' @name plotRLE
#' @export
#' @docType methods
#' @rdname plotRLE
setGeneric("plotRLE", function(object, ...) {
    standardGeneric("plotRLE")
})