From 2af0aceec9c0756dadf17d082c04cd310dcc910f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Xavier=20Escrib=C3=A0=20Montagut?=
 <xavier.escriba.montagut@gmail.com>
Date: Mon, 23 Jan 2023 16:14:26 +0100
Subject: [PATCH] docs: added NS

---
 NAMESPACE       |  1 +
 man/limmaDS2.Rd | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 man/limmaDS2.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 874aadb..e14c06b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -42,6 +42,7 @@ export(getChromosomeNamesDS)
 export(getSNPSbyGenDS)
 export(getVariable)
 export(limmaDS)
+export(limmaDS2)
 export(make_valid_namesDS)
 export(nFeaturesDS)
 export(nSamplesDS)
diff --git a/man/limmaDS2.Rd b/man/limmaDS2.Rd
new file mode 100644
index 0000000..e597e86
--- /dev/null
+++ b/man/limmaDS2.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/limmaDS2.R
+\name{limmaDS2}
+\alias{limmaDS2}
+\title{Differential expression analysis using limma on the server-side}
+\usage{
+limmaDS2(Set, res, type, contrasts, coef, annotCols, robust, sort.by)
+}
+\arguments{
+\item{Set}{either a \code{ExpressionSet} or a \code{RangedSummarizedExperiment}}
+
+\item{type}{...}
+
+\item{contrasts}{...}
+
+\item{coef}{...}
+
+\item{annotCols}{variables from the annotation data used in the output}
+
+\item{robust}{Logical value indicating whether robust method is applied in the eBayes function of limma. Default is FALSE.}
+
+\item{variable_names}{grouping variable used to perform differential expression analysis}
+
+\item{covariable_names}{name of variables used in the adjusted models}
+
+\item{levels}{...}
+
+\item{sva}{should differential expression analysis be adjusted by SVA?}
+
+\item{method}{String indicating the method used in the regression (e.g. lmFit function of limma: "ls" or 
+"robust". (Default: "ls")}
+
+\item{normalization}{String indicating the normalize method used when using voom for RNAseq data (see normalized.method argument in limma::vomm)}
+
+\item{voomQualityWeights}{Logical value indicating whether limma::voomWithQualityWeights should be used instead of
+limma::voom.}
+
+\item{big}{Logical value indicating whether SmartSVA should be used instead of SVA 
+(TRUE recommended for methylation or when having large number of samples).}
+}
+\value{
+a matrix with genes ordered by p-value
+}
+\description{
+Performs differential expression analysis using LIMMA
+}
+\author{
+Gonzalez, JR.
+}