% 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]]

}