R/PharmacoSet-accessors.R

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

## Navigating this file:
## - Slot section names start with ----
## - Method section names start with ==
##
## As a result, you can use Ctrl + f to find the slot or method you are looking
## for quickly, assuming you know its name.
##
## For example Ctrl + f '== molecularProfiles' would take you the molecularProfiles
## method, while Ctrl +f '---- molecularProfiles' would take you to the slot
## section.

#' @include PharmacoSet-class.R
NULL

## Variables for dynamic inheritted roxygen2 docs

.local_class <- 'PharmacoSet'
.local_data <- 'CCLEsmall'

#### CoreGx inherited methods
####
#### Note: The raw documentation lives in CoreGx, see the functions called
#### in @eval tags for the content of the metaprogrammed roxygen2 docs.
####
#### See .parseToRoxygen method in utils-messages.R file of CoreGx to
#### create similar metaprogrammed docs.
####
#### Warning: for dynamic docs to work, you must set
#### Roxygen: list(markdown = TRUE, r6=FALSE)
#### in the DESCRPTION file!


#' @title .parseToRoxygen
#'
#' @description
#' Helper for metaprogramming roxygen2 documentation
#'
#' @details
#' Takes a string block of roxygen2 tags sepearated by new-line
#'   characteres and parses it to the appropriate format for the @eval tag,
#'   subtituting any string in { } for the argument of the same name in `...`.
#'
#' @keywords internal
#' @importFrom CoreGx .parseToRoxygen
#' @export
#' @noRd
.parseToRoxygen <- function(string, ...) {
    CoreGx::.parseToRoxygen(string, ...)
}


# =======================================
# Accessor Method Documentation Object
# ---------------------------------------


#' @name PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_accessors(class_=.local_class)
#' @eval .parseToRoxygen(
#'      "@examples data({data_})
#'      ", data_=.local_data)
#' @importFrom methods callNextMethod
NULL


# ======================================
# Accessor Methods
# --------------------------------------


## ==============
## ---- drug slot
## --------------


##
## == drugInfo

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_treatmentInfo(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx treatmentInfo
#' @aliases drugInfo
#' @export
drugInfo <- function(...) treatmentInfo(...)

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_treatmentInfo(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx treatmentInfo<-
#' @aliases drugInfo<-
#' @export
`drugInfo<-` <- function(..., value) `treatmentInfo<-`(..., value=value)



##
## == drugNames


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_treatmentNames(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx treatmentNames
#' @aliases drugNames
#' @export
drugNames <- function(...) treatmentNames(...)



#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_treatmentNames(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx treatmentNames<-
#' @aliases drugNames<-
#' @export
`drugNames<-` <- function(..., value) `treatmentNames<-`(..., value=value)




## ====================
## ---- annotation slot
## --------------------


##
## == annotation


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_annotation(class_=.local_class, data_=.local_data)
#' @importMethodsFrom CoreGx annotation
#' @export
setMethod('annotation', signature("PharmacoSet"), function(object) {
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_annotation(class_=.local_class, data_=.local_data)
#' @importMethodsFrom CoreGx annotation<-
#' @export
setReplaceMethod("annotation", signature("PharmacoSet", "list"),
        function(object, value) {
    callNextMethod(object=object, value=value)
})


##
## == dateCreated


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_dateCreated(class_=.local_class, data_=.local_data)
#' @importMethodsFrom CoreGx dateCreated
#' @export
setMethod('dateCreated', signature("PharmacoSet"), function(object) {
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_dateCreated(class_=.local_class, data_=.local_data)
#' @importMethodsFrom CoreGx dateCreated<-
#' @export
setReplaceMethod('dateCreated', signature(object="PharmacoSet", value="character"),
        function(object, value) {
    callNextMethod(object=object, value=value)
})


##
## === name


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_name(class_=.local_class, data_=.local_data)
#' @importMethodsFrom CoreGx name
setMethod('name', signature("PharmacoSet"), function(object){
    callNextMethod(object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_name(class_=.local_class, data_=.local_data)
#' @importMethodsFrom CoreGx name<-
setReplaceMethod('name', signature("PharmacoSet"), function(object, value){
    object <- callNextMethod(object, value=value)
    return(invisible(object))
})

## ==============
## ---- sample slot
## --------------


##
## == sampleInfo

.local_sample <- "cell"

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sampleInfo(class_=.local_class, sample_=.local_sample)
#' @importFrom CoreGx sampleInfo
#' @export
setMethod("sampleInfo", "PharmacoSet", function(object) {
    callNextMethod(object)
})


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sampleInfo(class_=.local_class,
#' data_=.local_data, sample_="cell")
#' @importFrom CoreGx sampleInfo<-
#' @export
setReplaceMethod("sampleInfo", signature(object="PharmacoSet",
        value="data.frame"), function(object, value) {
    callNextMethod(object, value=value)
})


##
## == sampleNames


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sampleNames(class_=.local_class,
#' data_=.local_data, sample_=.local_sample)
#' @importMethodsFrom CoreGx sampleNames
setMethod("sampleNames", signature("PharmacoSet"), function(object) {
    callNextMethod(object)
})


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sampleNames(class_=.local_class,
#' data_=.local_data, sample_=.local_sample)
#' @importMethodsFrom CoreGx sampleNames<-
setReplaceMethod("sampleNames", signature(object="PharmacoSet", value="character"),
        function(object, value) {
    callNextMethod(object=object, value=value)
})



## ------------------
## ---- curation slot


##
## == curation


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_curation(class_=.local_class,
#' data_=.local_data, details_="Contains three `data.frame`s, 'cell' with
#' cell-line ids and 'tissue' with tissue ids and 'drug' with drug ids.")
#' @importMethodsFrom CoreGx curation
setMethod('curation', signature(object="PharmacoSet"), function(object) {
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_curation(class_=.local_class,
#' data_=.local_data, details_="For a `PharmacoSet` object the slot should
#' contain tissue, cell-line and drug id `data.frame`s.")
#' @importMethodsFrom CoreGx curation<-
setReplaceMethod("curation", signature(object="PharmacoSet", value="list"),
    function(object, value)
{
    callNextMethod(object=object, value=value)
})


## ----------------------
## ---- datasetType slot


#
# == datasetType


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_datasetType(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx datasetType
setMethod("datasetType", signature("PharmacoSet"), function(object) {
    callNextMethod(object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_datasetType(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx datasetType<-
setReplaceMethod("datasetType", signature(object="PharmacoSet",
    value='character'), function(object, value)
{
    callNextMethod(object=object, value=value)
})


## ---------------------------
## ---- molecularProfiles slot


##
## == molecularProfiles


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_molecularProfiles(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx molecularProfiles
setMethod(molecularProfiles, "PharmacoSet", function(object, mDataType, assay)
{
    callNextMethod()
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_molecularProfiles(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx molecularProfiles<-
setReplaceMethod("molecularProfiles", signature(object="PharmacoSet",
    mDataType ="character", assay="character", value="matrix"),
    function(object, mDataType, assay, value)
{
    callNextMethod(object=object, mDataType=mDataType, assay=assay, value=value)
})
setReplaceMethod("molecularProfiles",
    signature(object="PharmacoSet", mDataType ="character", assay="missing",
        value="matrix"), function(object, mDataType, assay, value)
{
    callNextMethod(object=object, mDataType=mDataType, assay=assay, value=value)
})


##
## == featureInfo


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_featureInfo(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx featureInfo
setMethod(featureInfo, "PharmacoSet", function(object, mDataType) {
    callNextMethod(object=object, mDataType=mDataType)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_featureInfo(class_=.local_class,
#' data_=.local_data, mDataType_='rna')
#' @importMethodsFrom CoreGx featureInfo<-
setReplaceMethod("featureInfo", signature(object="PharmacoSet",
    mDataType ="character",value="data.frame"),
    function(object, mDataType, value)
{
    callNextMethod(object=object, mDataType=mDataType, value=value)
})
setReplaceMethod("featureInfo", signature(object="PharmacoSet",
    mDataType ="character",value="DataFrame"),
    function(object, mDataType, value)
{
    callNextMethod(object=object, mDataType=mDataType, value=value)
})



##
## == phenoInfo


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_phenoInfo(class_=.local_class,
#' data_=.local_data, mDataType_='rna')
#' @importMethodsFrom CoreGx phenoInfo
setMethod('phenoInfo', signature(object='PharmacoSet', mDataType='character'),
    function(object, mDataType)
{
    callNextMethod(object=object, mDataType=mDataType)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_phenoInfo(class_=.local_class,
#' data_=.local_data, mDataType_='rna')
#' @importMethodsFrom CoreGx phenoInfo<-
setReplaceMethod("phenoInfo", signature(object="PharmacoSet",
    mDataType ="character", value="data.frame"),
    function(object, mDataType, value)
{
    callNextMethod(object=object, mDataType=mDataType, value=value)
})
setReplaceMethod("phenoInfo", signature(object="PharmacoSet",
    mDataType ="character", value="DataFrame"),
    function(object, mDataType, value)
{
    callNextMethod(object=object, mDataType=mDataType, value=value)
})


##
## == fNames


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_fNames(class_=.local_class,
#' data_=.local_data, mDataType_='rna')
#' @importMethodsFrom CoreGx fNames
setMethod('fNames', signature(object='PharmacoSet', mDataType='character'),
    function(object, mDataType)
{
    callNextMethod(object=object, mDataType=mDataType)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_fNames(class_=.local_class,
#' data_=.local_data, mDataType_='rna')
#' @importMethodsFrom CoreGx fNames<-
setReplaceMethod('fNames', signature(object='PharmacoSet', mDataType='character',
    value='character'), function(object, mDataType, value)
{
    callNextMethod(object=object, mDataType=mDataType, value=value)
})


##
## == mDataNames


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_mDataNames(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx mDataNames
setMethod("mDataNames", "PharmacoSet", function(object){
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_mDataNames(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx mDataNames<-
setReplaceMethod("mDataNames", "PharmacoSet", function(object, value){
    callNextMethod(object=object, value=value)
})



##
## == molecularProfilesSlot


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_molecularProfilesSlot(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx molecularProfilesSlot
setMethod("molecularProfilesSlot", signature("PharmacoSet"), function(object) {
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_molecularProfilesSlot(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx molecularProfilesSlot<-
setReplaceMethod("molecularProfilesSlot", signature("PharmacoSet", "list_OR_MAE"),
    function(object, value)
{
    callNextMethod(object=object, value=value)
})


# ---------------------
## ---- sensitivity slot


##
## == sensitivityInfo

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sensitivityInfo(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityInfo
setMethod('sensitivityInfo', signature("PharmacoSet"),
    function(object, dimension, ...)
{
    callNextMethod(object=object, dimension=dimension, ...)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sensitivityInfo(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityInfo<-
setReplaceMethod("sensitivityInfo", signature(object="PharmacoSet",
    value="data.frame"), function(object, dimension, ..., value)
{
    callNextMethod(object=object, dimension=dimension, ..., value=value)
})


##
## == sensitvityMeasures


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sensitivityMeasures(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityMeasures
setMethod('sensitivityMeasures', signature(object="PharmacoSet"),
    function(object)
{
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sensitityMeasures(class_=.local_class,
#' data_=.local_data)
setReplaceMethod('sensitivityMeasures',
    signature(object='PharmacoSet', value='character'), function(object, value)
{
    callNextMethod(object=object, value=value)
})


##
## == sensitivityProfiles


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sensitivityProfiles(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityProfiles
setMethod('sensitivityProfiles', signature(object="PharmacoSet"), function(object)
{
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sensitivityProfiles(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityProfiles<-
setReplaceMethod("sensitivityProfiles",
    signature(object="PharmacoSet", value="data.frame"),
    function(object, value)
{
    callNextMethod(object=object, value=value)
})


#
# == sensitivityRaw


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sensitivityRaw(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityRaw
setMethod("sensitivityRaw", signature("PharmacoSet"), function(object) {
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sensitivityRaw(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensitivityRaw<-
setReplaceMethod('sensitivityRaw', signature("PharmacoSet", "array"),
    function(object, value)
{
    callNextMethod(object=object, value=value)
})

#
# == treatmentResponse


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_treatmentResponse(class_=.local_class,
#'   data_=.local_data)
#' @importMethodsFrom CoreGx treatmentResponse
setMethod("treatmentResponse", signature("PharmacoSet"), function(object) {
    callNextMethod(object=object)
})



#' @rdname PharmacoSet-accessors
#' @importMethodsFrom CoreGx treatmentResponse<-
#' @eval CoreGx:::.docs_CoreSet_set_treatmentResponse(class_=.local_class,
#' data_=.local_data)
setReplaceMethod('treatmentResponse', signature(object='PharmacoSet',
    value='list_OR_LongTable'), function(object, value)
{
    callNextMethod(object=object, value=value)
})


##
## == sensNumber


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_sensNumber(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensNumber
setMethod('sensNumber', "PharmacoSet", function(object){
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_sensNumber(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx sensNumber<-
setReplaceMethod('sensNumber', signature(object="PharmacoSet", value="matrix"),
    function(object, value)
{
    callNextMethod(object=object, value=value)
})


## ======================
## ---- perturbation slot


##
## == pertNumber


#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_get_pertNumber(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx pertNumber
setMethod('pertNumber', signature(object='PharmacoSet'), function(object) {
    callNextMethod(object=object)
})

#' @rdname PharmacoSet-accessors
#' @eval CoreGx:::.docs_CoreSet_set_pertNumber(class_=.local_class,
#' data_=.local_data)
#' @importMethodsFrom CoreGx pertNumber<-
setReplaceMethod('pertNumber', signature(object='PharmacoSet', value="array"),
    function(object, value)
{
    callNextMethod(object=object, value=value)
})