R/loadGeneList.R

In WebGestaltR: Gene Set Analysis Toolkit WebGestaltR

loadInterestGene <- function(organism = "hsapiens", dataType = "list", inputGeneFile = NULL, inputGene = NULL, geneType = "entrezgene", collapseMethod = "mean", cache = NULL, hostName = "https://www.webgestalt.org/", geneSet) {
    if (is.null(inputGeneFile) && is.null(inputGene)) {
        stop(interestGeneError(type = "empty"))
    } else {
        if (organism != "others") {
            if (is.null(geneType)) {
                stop(interestGeneError(type = "emptyType"))
            } else {
                mapRe <- .uploadGeneExistingOrganism(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene, geneType = geneType, collapseMethod = collapseMethod, geneSet = geneSet, cache = cache, hostName = hostName)
            }
        } else {
            mapRe <- .uploadGeneOthers(dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene, geneSet = geneSet)
        }
    }

    # if organism is not others, the function will return a mapping result with mapped and unmapped list
    # if organism is others, the function will return a matrix with gene list
    return(mapRe)
}

#' @importFrom httr content
#' @importFrom readr read_tsv
loadReferenceGene <- function(organism = "hsapiens", referenceGeneFile = NULL, referenceGene = NULL, referenceGeneType = "entrezgene", referenceSet = NULL, collapseMethod = "mean", hostName = "https://www.webgestalt.org/", geneSet, interestGeneList, cache = NULL) {
    referenceGeneList <- NULL
    referenceGeneMap <- NULL

    if (is.null(referenceGeneFile) && is.null(referenceGene) && is.null(referenceSet)) {
        stop(referenceGeneError(type = "empty"))
    } else {
        if (organism != "others") {
            if (!is.null(referenceGeneFile) || !is.null(referenceGene)) {
                if (is.null(referenceGeneType)) {
                    stop(referenceGeneError(type = "emptyType"))
                } else {
                    mapRe <- .uploadGeneExistingOrganism(organism = organism, dataType = "list", inputGeneFile = referenceGeneFile, inputGene = referenceGene, geneType = referenceGeneType, collapseMethod = collapseMethod, geneSet = geneSet, cache = cache, hostName = hostName)
                    geneStandardId <- identifyStandardId(hostName = hostName, idType = referenceGeneType, organism = organism, type = "interest", cache = cache)
                    referenceGeneList <- mapRe$mapped[[geneStandardId]]
                }
            } else { ### referenceGeneFile and referenceGene are both NULL. But referenceSet is not NULL
                refS <- listReferenceSet(organism = organism, hostName = hostName, cache = cache)
                if (length(which(refS == referenceSet)) == 0) {
                    stop(referenceGeneError(type = "existingRef"))
                }
                refStandardId <- identifyStandardId(hostName = hostName, idType = referenceSet, organism = organism, type = "reference", cache = cache)
                if (startsWith(hostName, "file://")) {
                    # Getting data from local directory in the old way
                    refPath <- removeFileProtocol(file.path(hostName, "reference", paste0(paste(organism, referenceSet, refStandardId, sep = "_"), ".table")))
                    referenceGeneList <- read_tsv(refPath, col_names = FALSE, col_types = "c-")[[1]]
                } else {
                    response <- cacheUrl(file.path(hostName, "api", "reference"), cache = cache, query = list(organism = organism, referenceSet = referenceSet, standardId = refStandardId))
                    if (response$status_code != 200) {
                        stop(webRequestError(response))
                    }
                    # API now just returns one single column
                    referenceGeneList <- read_tsv(content(response), col_names = FALSE, col_types = "c")[[1]]
                }
            }
        } else { ## For other organisms
            if (!is.null(referenceGeneFile) || !is.null(referenceGene)) {
                referenceGeneList <- .uploadGeneOthers(dataType = "list", inputGeneFile = referenceGeneFile, inputGene = referenceGene, geneSet = geneSet)
                referenceGeneList <- unique(referenceGeneList)
            } else {
                stop(referenceGeneError(type = "empty"))
            }
        }
    }

    ## compare interest gene list and reference gene list
    if (length(intersect(interestGeneList, intersect(referenceGeneList, geneSet$gene))) == 0) {
        stop(referenceGeneError(type = "interestEmpty"))
    }
    return(referenceGeneList)
}


#' @importFrom dplyr filter
.uploadGeneExistingOrganism <- function(organism, dataType, inputGeneFile, inputGene, geneType, collapseMethod, geneSet, cache, hostName) {
    geneMap <- idMapping(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene, sourceIdType = geneType, targetIdType = NULL, collapseMethod = collapseMethod, mappingOutput = FALSE, cache = cache, hostName = hostName)

    # gene_standardId <- identifyStandardId(hostName=hostName,idtype=geneType,organism=organism,type="interest")  ##identifyStandardId in idMappingComponent.R
    # if(gene_standardId!=databaseStandardId){  ###the standardId of the input genes should be the same with the standardarId of the functional database
    # 	return(interestGeneError(type="unmatch"))
    # }

    geneMapMappedList <- geneMap$mapped
    standardId <- geneMap$standardId

    geneList <- as.character(unique(geneMapMappedList[[standardId]]))
    ov <- intersect(geneList, geneSet$gene)

    if (length(ov) == 0) {
        stop(interestGeneError(type = "unannotated"))
    }

    ### Because if all genes are annotated to only one category, GSEA will return the error, we need to avoid this error by reporting the error in the R#
    geneSets <- unique((filter(geneSet, .data$gene %in% geneList))[["geneSet"]])
    if (length(geneSets) == 1) {
        stop(interestGeneError(type = "onlyOne"))
    }
    return(geneMap)
}


#' @importFrom dplyr filter
.uploadGeneOthers <- function(dataType, inputGeneFile, inputGene, geneSet) {
    inputGene <- formatCheck(dataType = dataType, inputGeneFile = inputGeneFile, inputGene = inputGene)

    if (dataType == "list") {
        geneList <- inputGene
    } else if (dataType == "rnk") {
        geneList <- inputGene$gene
    }

    ov <- intersect(geneList, geneSet$gene)
    if (length(ov) == 0) {
        stop(interestGeneError(type = "unannotated"))
    }

    ### Because if all genes are annotated to only one category, GSEA will return the error, we need to avoid this error by reporting the error in the R#
    geneSets <- unique((filter(geneSet, .data$gene %in% geneList))[["geneSet"]])
    if (length(geneSets) == 1) {
        stop(interestGeneError(type = "onlyOne"))
    }
    return(inputGene)
}