R/GifyResult.R

In emreg00/guildifyR: GUILDify R

# GifyResult class containing data from GUILDify results 
# Data types for GifyResult class definition
setClassUnion("characterOrNULL", members=c("character", "NULL"))
setClassUnion("integerOrNULL", members=c("integer", "NULL"))

# GifyResult class definition
setClass("GifyResult",
    slots = c(scores="data.frame", 
	      functions="data.frame", 
	      functions2="data.frame", 
	      drugs="data.frame", 
	      cutoff="integerOrNULL",
	      job.id="characterOrNULL",
	      job.id2="characterOrNULL"),
    prototype = list(cutoff=NULL, job.id=NULL, job.id2=NULL)
)

# GifyResult constructor
GifyResult <- function(score.table, function.table, function.table2, drug.table, enrichment.cutoff, job.id, job.id2)
    new("GifyResult", scores=score.table, functions=function.table, functions2=function.table2, drugs=drug.table, cutoff=enrichment.cutoff, job.id=job.id, job.id2=job.id2)

setGeneric("gScores", function(x) standardGeneric("gScores"))
#' @export
#' @keywords internal
setMethod("gScores", "GifyResult", function(x) x@scores)

setGeneric("gFunctions", function(x) standardGeneric("gFunctions"))
#' @export
#' @keywords internal
setMethod("gFunctions", "GifyResult", function(x) x@functions)

setGeneric("gFunctions2", function(x) standardGeneric("gFunctions2"))
#' @export
#' @keywords internal
setMethod("gFunctions2", "GifyResult", function(x) x@functions2)

setGeneric("gDrugs", function(x) standardGeneric("gDrugs"))
#' @export
#' @keywords internal
setMethod("gDrugs", "GifyResult", function(x) x@drugs)

setGeneric("gCutoff", function(x) standardGeneric("gCutoff"))
#' @export
#' @keywords internal
setMethod("gCutoff", "GifyResult", function(x) x@cutoff)

setGeneric("gId", function(x) standardGeneric("gId"))
#' @export
#' @keywords internal
setMethod("gId", "GifyResult", function(x) x@job.id)

setGeneric("gId2", function(x) standardGeneric("gId2"))
#' @export
#' @keywords internal
setMethod("gId2", "GifyResult", function(x) x@job.id2)

setMethod("length", "GifyResult", function(x) sprintf("%d top-ranking proteins, %d functions, %d drugs", nrow(x@scores), nrow(x@functions), nrow(x@drugs)))

setMethod("show", "GifyResult", function(object) cat(class(object), "instance with", length(object), "\n"))

setValidity("GifyResult",
    function(object)
    {
        if (ncol(object@scores) != 6 & ncol(object@scores) != 4)
            return(sprintf("'scores' table does not have proper shape: (%d %d)", nrow(object@scores), ncol(object@scores)))
        if (ncol(object@functions) != 5)
            return("'functions' table must have 5 columns")
        #if (ncol(object@drugs) != 6) # Most species do not have drug info
        #    return("'drugs' table must have 6 columns")
        if (!is.null(object@cutoff))
	    if (object@cutoff == 0)
		message("Functional enrichment based top ranking cutoff is 0!")
	    if (!(object@cutoff >= 0))
		return(paste0("'cutoff' has invalid value", ": ", cutoff))
        #if (!is.null(object@job.id)) # there are custom job.ids as well
	#    if (nchar(object@job.id) != 36)
	#	return("'job.id' must have 36 characters")
        #if (!is.null(object@job.id2))
	#    if(nchar(object@job.id2) != 36)
	#	return("'job.id2' must have 36 characters")
        TRUE
    }
)


#setAs("GifyResult", "data.frame",
#function(from) from@scores 
#    # data.frame(functions=from@functions$go.id[1:20], drugs=from@drugs$drugbank.id[1:20])
#      )