--- a
+++ b/man/twoclasslimma.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runDEA.R
+\name{twoclasslimma}
+\alias{twoclasslimma}
+\title{Run two class comparison}
+\usage{
+twoclasslimma(
+  moic.res = NULL,
+  norm.expr = NULL,
+  prefix = NULL,
+  overwt = FALSE,
+  sort.p = TRUE,
+  verbose = TRUE,
+  res.path = getwd()
+)
+}
+\arguments{
+\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{norm.expr}{A matrix of normalized expression data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.}
+
+\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 limma
+}
+\description{
+Two class differential expression analysis using limma algorithm.
+}
+\details{
+twoclasslimma
+}
+\examples{
+# There is no example and please refer to vignette.
+}
+\references{
+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.
+}
+\keyword{internal}