#' K2 object
#'
#' This class is the output of K2preproc().
#' @slot eMat A numeric matrix comprising expression data used for partitioning
#' @slot eMatDS A numeric matrix comprising expression data used for differential expression
#' @slot gMat A numeric matrix comprising the output of runGeneSetScores().
#' @slot results A named list object containing results from each partition
#' @slot colData A data frame containing observation level data
#' @slot meta A named list containing different parameters used in workflow
#' @slot genesets A named list containing gene sets
#' @slot gene2Pathway Vector of collapsed gene set for which each gene belongs
#' @slot dataMatrix A numeric matrix used for different partitioning tasks
#' @slot geneURL A named list containing URLs for each gene
#' @slot genesetURL A named list containing URLs for each gene set
#' @keywords clustering
#' @export
setClassUnion("matrixORdgCMatrix", c("matrix", "dgCMatrix"))
setClass("K2", slots = c(meta="list",
eMat="matrixORdgCMatrix",
eMatDS ="matrixORdgCMatrix",
gMat="matrixORdgCMatrix",
colData = "data.frame",
dataMatrix="matrixORdgCMatrix",
results="list",
genesets="list",
gene2Pathway="character",
geneURL="character",
genesetURL="character"))
setMethod("show", "K2", function(object) {
cat("K2Taxonomer results:", "\n",
" Expression Data: ", ifelse(
ncol(object@eMat) == 0, "FALSE", "TRUE"), "\n",
" Pre-processing: ", ifelse(
length(object@meta) == 0 &
ncol(object@dataMatrix) == 0 &
ncol(object@colData) == 0,
"FALSE", "TRUE"), "\n",
" Recursive partitioning: ", ifelse(
length(object@results) == 0, "FALSE", "TRUE"),
"\n",
" Differential Gene Expression: ", ifelse(
is.null(object@results$A$dge), "FALSE", "TRUE"),
"\n",
" Gene Set Hyperenrichment: ", ifelse(
is.null(object@results$A$gse), "FALSE", "TRUE"),
"\n",
" Single-sample Enrichment: ", ifelse(
ncol(object@gMat) == 0, "FALSE", "TRUE"),
"\n",
" Differential Enrichment Analysis: ", ifelse(
is.null(object@results$A$dsse), "FALSE", "TRUE"),
"\n", sep = ""
)
})
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