R/accessor.R

In clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

##' @method as.data.frame compareClusterResult
##' @export
as.data.frame.compareClusterResult <- getFromNamespace("as.data.frame.compareClusterResult", "enrichplot")

##' @method as.data.frame groupGOResult
##' @export
as.data.frame.groupGOResult <- function(x, ...) {
    as.data.frame(x@result, ...)
}

##' @method [ compareClusterResult
##' @export
`[.compareClusterResult` <- function(x, i, j, asis = FALSE, ...) {
    result <- as.data.frame(x)
    y <- result[i,j, ...]
    if (!asis)
        return(y)
    x@compareClusterResult <- y
    return(x)
}

##' @method [[ compareClusterResult
##' @export
`[[.compareClusterResult` <- function(x, i) {
    ## gc <- geneInCategory(x)
    ## if (!i %in% names(gc))
    ##     stop("input term not found...")
    ## gc[[i]]

    idx <- which(i == x[, "ID"])
    if (length(idx) == 0) 
        stop("input term not found...")

    y <- x[idx, asis = TRUE]
    geneInCategory(y)
}


##' @importFrom utils head
##' @method head compareClusterResult
##' @export
head.compareClusterResult <- function(x, n=6L, ...) {
    head(as.data.frame(x), n, ...)
}


##' @importFrom utils tail
##' @method tail compareClusterResult
##' @export
tail.compareClusterResult <- function(x, n=6L, ...) {
    tail(as.data.frame(x), n, ...)
}


##' @method dim compareClusterResult
##' @export
dim.compareClusterResult <- function(x) {
    dim(as.data.frame(x))
}


##' @method geneID groupGOResult
##' @importFrom DOSE geneID
##' @export
geneID.groupGOResult <- function(x) as.character(x@result$geneID)


##' @method geneInCategory groupGOResult
##' @export
##' @importFrom DOSE geneInCategory
##' @importFrom stats setNames
geneInCategory.groupGOResult <- function(x)
    setNames(strsplit(geneID(x), "/", fixed=TRUE), rownames(x@result))