--- a
+++ b/man/runDEA.Rd
@@ -0,0 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runDEA.R
+\name{runDEA}
+\alias{runDEA}
+\title{Run differential expression analysis}
+\usage{
+runDEA(
+  dea.method = c("deseq2", "edger", "limma"),
+  expr = NULL,
+  moic.res = NULL,
+  prefix = NULL,
+  overwt = FALSE,
+  sort.p = TRUE,
+  verbose = TRUE,
+  res.path = getwd()
+)
+}
+\arguments{
+\item{dea.method}{A string value to indicate the algorithm for differential expression analysis. Allowed value contains c('deseq2', 'edger', 'limma'). The former two require RNA-Seq raw count data and the last one requires normalized expression data (FPKM or TPM without log2 transformation is recommended).}
+
+\item{expr}{A matrix of expression data.}
+
+\item{moic.res}{An object returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms.}
+
+\item{prefix}{A string value to indicate the prefix of output file.}
+
+\item{overwt}{A logic value to indicate if to overwrite existing results; FALSE by default.}
+
+\item{sort.p}{A logic value to indicate if to sort adjusted p value for output table; TRUE by default.}
+
+\item{verbose}{A logic value to indicate if to only output id, log2fc, pvalue, and padj; TRUE by default.}
+
+\item{res.path}{A string value to indicate the path for saving the results.}
+}
+\value{
+Several .txt files storing differential expression analysis results by specified algorithm
+}
+\description{
+Using choosen algorithm to run differential expression analysis between two classes identified by multi-omics clustering process.
+}
+\details{
+runDEA
+}
+\examples{
+# There is no example and please refer to vignette.
+}
+\references{
+Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15(12):550-558.
+
+Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139-140.
+
+McCarthy DJ, Chen Y, Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40(10):4288-4297.
+
+Ritchie, ME, Phipson, B, Wu, D, Hu, Y, Law, CW, Shi, W, and Smyth, GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res, 43(7):e47.
+}