R/classfCI.R

In fCI: f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

#' An S4 class to represent a bank account.
#'
#' @sample.data.file A character string
setClass("NPCI",representation(
	sample.data.file="character",
	distance.matrix="matrix",
	sample.data.normalized="data.frame",
	attr.info="data.frame",
	null.data.start="matrix",
	diff.data.start="matrix",
	expr.by.fold="matrix",
	fold.cutoff.list="list",
	rank.index.to.be.removed="list",
	diff.gene.ids="list", 
	wt.index="numeric",
	df.index="numeric",
	ctr.indexes="numeric",
	trt.indexes="numeric",
	method.option="numeric",
	use.ratio="logical",
	percent.genes.to.scan="numeric",
	num.genes.to.skip.each="numeric",
	use.fold.change="logical",
	wt.comb="list",
	df.comb="list",
	diff.ids="list",
	result="numeric",
	indexes.reconsidered="numeric",
	center.by.gaussian.kernel="logical",
	symmetric.fold="logical",
	pairwise.diff.gene.ids="list")
)

setClass("fCI",representation(
	sample.data.file="character",
	distance.matrix="matrix",
	sample.data.normalized="data.frame",
	attr.info="data.frame",
	null.data.start="matrix",
	diff.data.start="matrix",
	expr.by.fold="matrix",
	fold.cutoff.list="list",
	rank.index.to.be.removed="list",
	diff.gene.ids="list", 
	wt.index="numeric",
	df.index="numeric",
	ctr.indexes="numeric",
	trt.indexes="numeric",
	method.option="numeric",
	use.ratio="logical",
	percent.genes.to.scan="numeric",
	num.genes.to.skip.each="numeric",
	use.fold.change="logical",
	wt.comb="list",
	df.comb="list",
	diff.ids="list",
	result="numeric",
	indexes.reconsidered="numeric",
	center.by.gaussian.kernel="logical",
	symmetric.fold="logical",
	pairwise.diff.gene.ids="list")
)