R/plageParam.R

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

#' @title The `plageParam` class
#'
#' @description Objects of class `plageParam` contain the parameters for running
#' the `PLAGE` method.
#'
#' @details `PLAGE` takes a number of parameters shared with all methods
#' implemented by package GSVA but does not take any method-specific parameters.
#' These parameters are described in detail below.
#'
#' @param exprData The expression data set.  Must be one of the classes
#' supported by [`GsvaExprData-class`].  For a list of these classes, see its
#' help page using `help(GsvaExprData)`.
#'
#' @param geneSets The gene sets.  Must be one of the classes supported by
#' [`GsvaGeneSets-class`].  For a list of these classes, see its help page using
#' `help(GsvaGeneSets)`.
#' 
#' @param assay Character vector of length 1.  The name of the assay to use in
#' case `exprData` is a multi-assay container, otherwise ignored.  By default,
#' the first assay is used.
#' 
#' @param annotation An object of class [`GeneIdentifierType-class`] from
#' package `GSEABase` describing the gene identifiers used as the row names of
#' the expression data set.  See [`GeneIdentifierType`] for help on available
#' gene identifier types and how to construct them.  This
#' information can be used to map gene identifiers occurring in the gene sets.
#' 
#' If the default value `NULL` is provided, an attempt will be made to extract
#' the gene identifier type from the expression data set provided as `exprData`
#' (by calling [`gsvaAnnotation`] on it).  If still not successful, the
#' `NullIdentifier()` will be used as the gene identifier type, gene identifier
#' mapping will be disabled and gene identifiers used in expression data set and
#' gene sets can only be matched directly.
#' 
#' @param minSize Numeric vector of length 1.  Minimum size of the resulting gene
#' sets after gene identifier mapping. By default, the minimum size is 1.
#' 
#' @param maxSize Numeric vector of length 1.  Maximum size of the resulting gene
#' sets after gene identifier mapping. By default, the maximum size is `Inf`.
#' 
#' @return A new [`plageParam-class`] object.
#'
#' @references Tomfohr, J. et al. Pathway level analysis of gene expression
#' using singular value decomposition.
#' *BMC Bioinformatics*, 6:225, 2005.
#' [DOI](https://doi.org/10.1186/1471-2105-6-225)
#'
#' @examples
#' library(GSVA)
#' library(GSVAdata)
#'
#' data(leukemia)
#' data(c2BroadSets)
#'
#' ## for simplicity, use only a subset of the sample data
#' ses <- leukemia_eset[1:1000, ]
#' gsc <- c2BroadSets[1:100]
#' pp1 <- plageParam(ses, gsc)
#' pp1
#'
#' @importFrom methods new
#' @rdname plageParam-class
#' 
#' @export
plageParam <- function(exprData, geneSets,
                       assay=NA_character_, annotation=NULL,
                       minSize=1, maxSize=Inf) {
    an <- gsvaAssayNames(exprData)
    if((!is.na(assay)) && (!.isCharNonEmpty(an))) {
        msg <- sprintf(paste0("argument assay='%s' ignored since exprData has ",
                              "no assayNames()"), assay)
        cli_alert_info(msg)
    }
    if(is.na(assay) && .isCharNonEmpty(an))
        assay <- na.omit(an)[1]

    ## check for presence of valid row/feature names
    .check_rownames(exprData)

    xa <- gsvaAnnotation(exprData)
    if(is.null(xa)) {
        if(is.null(annotation)) {
            annotation <- NullIdentifier()
        }
    } else {
        if(is.null(annotation)) {
            annotation <- xa
        } else {
            msg <- sprintf(paste0("using argument annotation='%s' and ",
                                  "ignoring exprData annotation ('%s')"),
                           capture.output(annotation), capture.output(xa))
            cli_alert_info(msg)
        }
    }

    new("plageParam", exprData=exprData, geneSets=geneSets,
        assay=assay, annotation=annotation,
        minSize=minSize, maxSize=maxSize)
}


## ----- validator -----

setValidity("plageParam", function(object) {
    inv <- NULL
    xd <- object@exprData
    dd <- dim(xd)
    an <- gsvaAssayNames(xd)
    oa <- object@assay
    
    if(dd[1] == 0) {
        inv <- c(inv, "@exprData has 0 rows")
    }
    if(dd[2] == 0) {
        inv <- c(inv, "@exprData has 0 columns")
    }
    if(length(object@geneSets) == 0) {
        inv <- c(inv, "@geneSets has length 0")
    }
    if(length(oa) != 1) {
        inv <- c(inv, "@assay must be of length 1")
    }
    if(.isCharLength1(oa) && .isCharNonEmpty(an) && (!(oa %in% an))) {
        inv <- c(inv, "@assay must be one of assayNames(@exprData)")
    }
    if(length(object@annotation) != 1) {
        inv <- c(inv, "@annotation must be of length 1")
    }
    if(!inherits(object@annotation, "GeneIdentifierType")) {
        inv <- c(inv, "@annotation must be a subclass of 'GeneIdentifierType'")
    }
    if(length(object@minSize) != 1) {
        inv <- c(inv, "@minSize must be of length 1")
    }
    if(object@minSize < 1) {
        inv <- c(inv, "@minSize must be at least 1 or greater")
    }
    if(length(object@maxSize) != 1) {
        inv <- c(inv, "@maxSize must be of length 1")
    }
    if(object@maxSize < object@minSize) {
        inv <- c(inv, "@maxSize must be at least @minSize or greater")
    }
    return(if(length(inv) == 0) TRUE else inv)
})