R/Class.R

In stela2502/RFclust.SGE: Unsupervised clustering using random forest run on SGE

#' @name RFclust.SGE
#' @title RFclust.SGE
#' @docType package
#' @description  An S4 class to run unsupervides clustering based on random forrest predictors using the Sun Grid Engine.
#' @slot dat the data that should be clustered (dgCMatrix with column ==  samples rows ==  observations)
#' @slot email the users email for the SGE report
#' @slot slices the number of slices the data should be analyzed in
#' @slot tmp.path the temp path for the clustering results
#' @slot SGE run using Sun Grid Engine (default= F)
#' @slot distRF the density data (internal use only)
#' @slot RFfiles an internal list of RF files (internal use only)
#' @slot name the name for this object that will be used to identify the data object in the spawned processes
#' @source \url{https://labs.genetics.ucla.edu/horvath/RFclustering/RFclustering.htm}
#' @exportClass RFclust.SGE
setClass(
    Class = 'RFclust.SGE',
    representation =  representation (
        dat = 'dgCMatrix',
        email = 'character',
        slices = 'numeric',
        tmp.path = 'character',
        SGE = 'logical',
        slurm = 'logical',
        settings = 'list',
        distRF = 'list',
        RFfiles = 'list',
        name = 'character',
	debug = 'logical'
    ),
    prototype(tmp.path = NA_character_,  email =  NA_character_,
        slices = 32, SGE= FALSE, distRF = list(), RFfiles = list(), settings = list(), debug =F
    )
)