R/upDownGene.R

In cogena: co-expressed gene-set enrichment analysis

#' Show up or down-regualted genes for a clustering method and the number of clusters.
#'
#' The value means up or down regulated genes for each cluster. 1 suggests that
#' genes in the cluster is up-regualted genes, while -1 down-regualted genes. 
#' value within (-1, 1) means genes there are both up and down regulated genes
#' in the cluster. Return a vector with the length of nCluster if add2 is 
#' FALSE, or the length of nCluster + 2 if add2 is TRUE and nCluster is not 2. 
#' In the latter situation, the last two itemes represent Up and Down
#' reuglated genes
#' 
#' @param object a genecl or cogena object
#' @param method as clMethods in genecl function
#' @param nCluster cluster number
#' @param add2 add2 enrichment score for add Up and Down reuglated genes
#' @return upDownGene: a vector
#' @rdname upDownGene
#' @export
#' 
#' @examples 
#' data(Psoriasis)
#' annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz", 
#' package="cogena")
#' 
#' 
#' genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"), 
#'     metric="correlation", method="complete", ncore=2, verbose=TRUE)
#' 
#' clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)
#' 
#' upDownGene(clen_res, "kmeans", "3", add2=TRUE)
#' 
#' upDownGene(clen_res, "kmeans", "2", add2=FALSE)
#' 
setGeneric("upDownGene", 
           function(object, method, nCluster, add2=FALSE) 
               standardGeneric("upDownGene"))

#' @rdname upDownGene
#' @aliases upDownGene,cogena
#' @import dplyr
setMethod("upDownGene", signature(object="cogena"), function(
    object, method, nCluster, add2=FALSE) {
    sampleLabel <- object@sampleLabel
    
    logFC <- NULL; cluster_id = NULL
    
    # Return a vector representing the up or down regulated genes. (1 or -1)
    geneExp <- as.data.frame(geneExpInCluster(object, method, nCluster)$clusterGeneExp)
    sampleLabel <- geneExpInCluster(object, method, nCluster)$label
    geneExp <- logfc(geneExp, sampleLabel)
    geneExp <- geneExp[,c("cluster_id", "logFC")]
    cluster_upDn <- dplyr::group_by(geneExp, cluster_id)
    cluster_upDn <- dplyr::summarise(cluster_upDn, UpDn=sum(logFC)/n() )
    cluster_upDn <- dplyr::arrange(cluster_upDn, cluster_id)
    cluster_logfc <- cluster_upDn$UpDn
    
    if (isTRUE(add2) ) {
        res <- c(cluster_logfc, c(1, -1))
    } else {
        res <- cluster_logfc
    }
    return (res)
})

#' logfc: add MeanA, MeanB and logFC to the dat
#' 
#' 
#' @param dat gene expression data frame
#' @param sampleLabel factor. sampleLabel with names
#' @return logfc: a data.frame
#' @rdname upDownGene
#' @aliases logfc, upDownGene
#' @export
# Add MeanA, MeanB and logFC.  
logfc <- function(dat, sampleLabel) {
    if (length(unique(sampleLabel)) != 2) {
        Biobase::note(paste0("Only first two labels \"", names(table(sampleLabel))[1], " and ", names(table(sampleLabel))[2], "\" are used for Up or Down-genes labeling as more than two labels exist!"))
    }
    dat$meanA <- apply(dat[,names(sampleLabel)[which((sampleLabel == names(table(sampleLabel))[1]))]], 1, mean)
    dat$meanB <- apply(dat[,names(sampleLabel)[which((sampleLabel == names(table(sampleLabel))[2]))]], 1, mean)
    # log2 transform
    if ( is.infinite(2**max(dat, na.rm =TRUE)) ) {
        dat$logFC <- ifelse( log2(dat$meanB/dat$meanA) > 0, 1, -1)
    } else {
        dat$logFC <- ifelse( (dat$meanB-dat$meanA) >0, 1, -1)
    }
    
    return (dat)
}