% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/DIscBIO-generic-DEGanalysis2clust.R

\name{DEGanalysis2clust}

\alias{DEGanalysis2clust}

\alias{DEGanalysis2clust,DISCBIO-method}

\title{Determining differentially expressed genes (DEGs) between two

  particular clusters.}

\usage{

DEGanalysis2clust(

  object,

  K,

  Clustering = "K-means",

  fdr = 0.05,

  name = "Name",

  First = "CL1",

  Second = "CL2",

  export = FALSE,

  quiet = FALSE,

  plot = TRUE,

  filename_deg = "DEGsTable",

  filename_sigdeg = "sigDEG",

  ...

)

\S4method{DEGanalysis2clust}{DISCBIO}(

  object,

  K,

  Clustering = "K-means",

  fdr = 0.05,

  name = "Name",

  First = "CL1",

  Second = "CL2",

  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{First}{A string vector showing the first target cluster.  Default is

"CL1"}

\item{Second}{A string vector showing the second target cluster.  Default is

"CL2"}

\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 particular clusters generated

  by either K-means or model based clustering.

}