--- a
+++ b/man/DEGanalysis.Rd
@@ -0,0 +1,69 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/DIscBIO-generic-DEGanalysis.R
+\name{DEGanalysis}
+\alias{DEGanalysis}
+\alias{DEGanalysis,DISCBIO-method}
+\title{Determining differentially expressed genes (DEGs) between all
+  individual clusters.}
+\usage{
+DEGanalysis(
+  object,
+  K,
+  Clustering = "K-means",
+  fdr = 0.05,
+  name = "Name",
+  export = FALSE,
+  quiet = FALSE,
+  plot = TRUE,
+  filename_deg = "DEGsTable",
+  filename_sigdeg = "sigDEG",
+  ...
+)
+
+\S4method{DEGanalysis}{DISCBIO}(
+  object,
+  K,
+  Clustering = "K-means",
+  fdr = 0.05,
+  name = "Name",
+  export = FALSE,
+  quiet = FALSE,
+  plot = TRUE,
+  filename_deg = "DEGsTable",
+  filename_sigdeg = "sigDEG",
+  ...
+)
+}
+\arguments{
+\item{object}{\code{DISCBIO} class object.}
+
+\item{K}{A numeric value of the number of clusters.}
+
+\item{Clustering}{Clustering has to be one of the following:
+["K-means","MB"]. Default is "K-means"}
+
+\item{fdr}{A numeric value of the false discovery rate. Default is 0.05.}
+
+\item{name}{A string vector showing the name to be used to save the resulted
+tables.}
+
+\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{plot}{if `TRUE`, plots are generated}
+
+\item{filename_deg}{Name of the exported DEG table}
+
+\item{filename_sigdeg}{Name of the exported sigDEG table}
+
+\item{...}{additional parameters to be passed to samr()}
+}
+\value{
+A list containing two tables.
+}
+\description{
+This function defines DEGs between all individual clusters
+  generated by either K-means or model based clustering.
+}