R/methods-tsRim.R

In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

# tsRim methods

setGeneric("rimMass", function(obj) standardGeneric("rimMass"))
setMethod("rimMass", "tsRim", function(obj) obj@mass)
setGeneric("rimMass<-", function(obj, value) standardGeneric("rimMass<-"))
setReplaceMethod("rimMass", "tsRim", function(obj, value) { obj@mass <- value
 validObject(obj)
 obj })

setGeneric("rimLimits", function(obj) standardGeneric("rimLimits"))
setMethod("rimLimits", "tsRim", function(obj) obj@limits)
setGeneric("rimLimits<-", function(obj, value) standardGeneric("rimLimits<-"))
setReplaceMethod("rimLimits", "tsRim", function(obj, value) { obj@limits <- value
 validObject(obj)
 obj })

setGeneric("rimStandard", function(obj) standardGeneric("rimStandard"))
setMethod("rimStandard", "tsRim", function(obj) obj@standard)
setGeneric("rimStandard<-", function(obj, value) standardGeneric("rimStandard<-"))
setReplaceMethod("rimStandard", "tsRim", function(obj, value) { obj@standard <- value
 validObject(obj)
 obj })

setValidity("tsRim", function(object) {
	if(ncol(object@limits) != 2)
		paste("Number of columns of limits it is not equal to 2")
	else if(nrow(object@limits) != length(object@standard))
		paste("Unequal number of standards and limits: ", length(object@standard),
			", ", nrow(object@limits), sep = "")
	else if(length(object@mass) != 1 & length(object@mass) != length(object@standard))
		paste("Unequal number of standards and mass markers: ", length(object@standard),
		", ", length(object@mass), sep = "")
	else TRUE
})

setMethod("[", "tsRim",
    function(x, i, j, ..., drop=TRUE)
    {
        if(missing(i) & missing(j)) {
            validObject(x)
            return(x)
        }
        if(!missing(j))
            stop("incorrect number of dimensions")

        if(is.character(i)) {
            if(is.null(rownames(x@limits)))
                stop("subscript out of bounds")
            i <- match(i, rownames(x@limits))
        }
        assert_that(noNA(i), msg="subscript out of bounds")

        x@limits <- x@limits[i,,drop=FALSE]
        x@standard <- x@standard[i]
        x@mass <- if(length(x@mass) == 1) x@mass else x@mass[i]
        validObject(x)
        return(x)
    }
)

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