--- a
+++ b/man/ClustDiffGenes.Rd
@@ -0,0 +1,68 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DIscBIO-generic-ClustDiffGenes.R
+\name{ClustDiffGenes}
+\alias{ClustDiffGenes}
+\alias{ClustDiffGenes,DISCBIO-method}
+\title{ClustDiffGenes}
+\usage{
+ClustDiffGenes(
+  object,
+  K,
+  pValue = 0.05,
+  fdr = 0.01,
+  export = FALSE,
+  quiet = FALSE,
+  filename_up = "Up-DEG-cluster",
+  filename_down = "Down-DEG-cluster",
+  filename_binom = "binomial-DEGsTable",
+  filename_sigdeg = "binomial-sigDEG"
+)
+
+\S4method{ClustDiffGenes}{DISCBIO}(
+  object,
+  K,
+  pValue = 0.05,
+  fdr = 0.01,
+  export = FALSE,
+  quiet = FALSE,
+  filename_up = "Up-DEG-cluster",
+  filename_down = "Down-DEG-cluster",
+  filename_binom = "binomial-DEGsTable",
+  filename_sigdeg = "binomial-sigDEG"
+)
+}
+\arguments{
+\item{object}{\code{DISCBIO} class object.}
+
+\item{K}{A numeric value of the number of clusters.}
+
+\item{pValue}{A numeric value of the p-value. Default is 0.05.}
+
+\item{fdr}{A numeric value of the false discovery rate. Default is 0.01.}
+
+\item{export}{A logical vector that allows writing the final gene list in
+excel file. Default is TRUE.}
+
+\item{quiet}{if `TRUE`, suppresses intermediate text output}
+
+\item{filename_up}{Name of the exported "up" file (if `export=TRUE`)}
+
+\item{filename_down}{Name of the exported "down" file (if `export=TRUE`)}
+
+\item{filename_binom}{Name of the exported binomial file}
+
+\item{filename_sigdeg}{Name of the exported sigDEG file}
+}
+\value{
+A list containing two tables.
+}
+\description{
+Creates a table of cluster differences
+}
+\examples{
+sc <- DISCBIO(valuesG1msTest)
+sc <- Clustexp(sc, cln = 3, quiet = TRUE)
+cdiff <- ClustDiffGenes(sc, K = 3, fdr = .3, export = FALSE)
+str(cdiff)
+cdiff[[2]]
+}