From babe0f0f74baeda4e05d25880fda72466bb5bc26 Mon Sep 17 00:00:00 2001
From: jsychong <jasmine.chong@mail.mcgill.ca>
Date: Wed, 6 Mar 2019 14:06:17 -0500
Subject: [PATCH] minor documentation updates

---
 man/PerformGSEA.Rd          | 6 +-----
 man/PerformMummichog.Rd     | 6 +-----
 man/PerformPeakProfiling.Rd | 5 ++++-
 3 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/man/PerformGSEA.Rd b/man/PerformGSEA.Rd
index 9097712d..6faaf68a 100644
--- a/man/PerformGSEA.Rd
+++ b/man/PerformGSEA.Rd
@@ -4,17 +4,13 @@
 \alias{PerformGSEA}
 \title{New main function to perform fast pre-ranked mummichog}
 \usage{
-PerformGSEA(mSetObj=NA, lib, enrichOpt, pvalOpt, permNum = 100)
+PerformGSEA(mSetObj=NA, lib, permNum = 100)
 }
 \arguments{
 \item{mSetObj}{Input the name of the created mSetObj object}
 
 \item{lib}{Input the name of the organism library, default is hsa}
 
-\item{enrichOpt}{Input the method to perform enrichment analysis}
-
-\item{pvalOpt}{Input the method to calculate p-values}
-
 \item{permNum}{Numeric, the number of permutations to perform}
 }
 \description{
diff --git a/man/PerformMummichog.Rd b/man/PerformMummichog.Rd
index eb8760f2..239ddbb3 100644
--- a/man/PerformMummichog.Rd
+++ b/man/PerformMummichog.Rd
@@ -4,17 +4,13 @@
 \alias{PerformMummichog}
 \title{Main function to perform mummichog}
 \usage{
-PerformMummichog(mSetObj=NA, lib, enrichOpt, pvalOpt, permNum = 100)
+PerformMummichog(mSetObj=NA, lib, permNum = 100)
 }
 \arguments{
 \item{mSetObj}{Input the name of the created mSetObj object}
 
 \item{lib}{Input the name of the organism library, default is hsa}
 
-\item{enrichOpt}{Input the method to perform enrichment analysis}
-
-\item{pvalOpt}{Input the method to calculate p-values}
-
 \item{permNum}{Numeric, the number of permutations to perform}
 }
 \description{
diff --git a/man/PerformPeakProfiling.Rd b/man/PerformPeakProfiling.Rd
index 484bb1d2..ed99d881 100644
--- a/man/PerformPeakProfiling.Rd
+++ b/man/PerformPeakProfiling.Rd
@@ -7,7 +7,8 @@ This function performs feature extraction of user's raw MS data using
 the rawData object created using the InspectRawMSData function.}
 \usage{
 PerformPeakProfiling(rawData, peakParams, rtPlot = TRUE,
-  pcaPlot = TRUE, format = "png", dpi = 72, width = 9)
+  pcaPlot = TRUE, labels = TRUE, format = "png", dpi = 72,
+  width = 9)
 }
 \arguments{
 \item{rawData}{The object created using the InspectRawMSData function,
@@ -23,6 +24,8 @@ Defaut is set to true.}
 \item{pcaPlot}{Logical, if true creates a PCA plot to evaluate the sample grouping.
 Default is set to true.}
 
+\item{labels}{Logical, if true, the PCA plot will be annotated with sample names.}
+
 \item{format}{Character, input the format of the image to create.}
 
 \item{dpi}{Numeric, input the dpi of the image to create.}