From 4bc7319ea59ce7851b81f253f14c5537dccb97fe Mon Sep 17 00:00:00 2001
From: Dong <yonghui.dong@gmail.com>
Date: Fri, 9 Apr 2021 17:51:34 +0300
Subject: [PATCH] rm getOPLSDA() function

---
 NAMESPACE        |  2 --
 R/doStat.R       |  3 +--
 R/getOPLSDA.R    | 44 --------------------------------------------
 man/getOPLSDA.Rd | 24 ------------------------
 4 files changed, 1 insertion(+), 72 deletions(-)
 delete mode 100644 R/getOPLSDA.R
 delete mode 100644 man/getOPLSDA.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 9cdf479..d3e1592 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,7 +11,6 @@ export(doStat)
 export(getCV)
 export(getFC)
 export(getMax)
-export(getOPLSDA)
 export(getP)
 export(mass)
 export(mz)
@@ -38,7 +37,6 @@ importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
 importFrom(reshape2,melt)
-importFrom(ropls,opls)
 importFrom(stats,TukeyHSD)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)
diff --git a/R/doStat.R b/R/doStat.R
index a9a730b..69ccc4d 100644
--- a/R/doStat.R
+++ b/R/doStat.R
@@ -16,8 +16,7 @@ doStat <- function(x, Group = NULL){
   myCV <- getCV(x, Group = Group)
   myFC <- getFC(x, Group = Group)
   myP <- getP(x, Group = Group)
-  myOPLSDA <- getOPLSDA(x, Group = Group)
-  myStat <- cbind(maxSample, myCV, myFC, myP, myOPLSDA)
+  myStat <- cbind(maxSample, myCV, myFC, myP)
   cat("\nStatistical analysis done. \n")
   rownames(myStat) <- colnames(x)
   return(myStat)
diff --git a/R/getOPLSDA.R b/R/getOPLSDA.R
deleted file mode 100644
index f4a9a0d..0000000
--- a/R/getOPLSDA.R
+++ /dev/null
@@ -1,44 +0,0 @@
-#' @title calculate VIP values
-#' @description calculate VIP values using among different samples groups using OPLSDA.
-#' @param x sample ion intensity matrix, row sample, column feature.
-#' @param Group sample group information
-#' @importFrom utils combn
-#' @importFrom ropls opls
-#' @return a dataframe with vip values
-#' @export
-#' @examples
-#' dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
-#' myGroup <- rep_len(LETTERS[1:3], 300)
-#' out <- getOPLSDA(dat, Group = myGroup)
-
-getOPLSDA <- function(x, Group = NULL){
-  cat("\n- Calculating VIP values...\n")
-  #(1) check input
-  Group <- as.factor(Group)
-  if(is.null(Group)){stop("Please include group information")}
-  if(length(levels(Group)) <= 1){stop("At least two sample groups should be included")}
-  if(length(Group) != nrow(x)){stop("Missing group informaiton detected")}
-
-  #(2) perform OPLS
-  n <- levels(Group)
-  dat2 <- cbind.data.frame(x, Group = Group)
-  mylist <- combn(n, 2, FUN = function(x) subset(dat2, Group %in% x), simplify = FALSE)
-  ## change mylist names
-  listnames <- combn(n, 2, simplify = FALSE)
-  names(mylist) <- lapply(listnames, function(x) paste("OPLSDA", paste(x, collapse="_vs_"), sep = "_"))
-  ## perform OPLS-DA using opls package
-  oplsdafun <- function(i) {
-    myVIP <- opls(x = subset(i, select = -Group),
-                  y = as.character(i$Group),
-                  predI = 1,
-                  orthoI = 1,
-                  permI = 10,
-                  crossvalI = min(nrow(i), 7),
-                  fig.pdfC = "none",
-                  info.txtC = "none")
-    round(myVIP@vipVn, 2)
-  }
-  list_VIP <- lapply(mylist, oplsdafun)
-  ## convert result to dataframe and keep the name
-  return(data.frame(list_VIP))
-}
diff --git a/man/getOPLSDA.Rd b/man/getOPLSDA.Rd
deleted file mode 100644
index fe5d0fc..0000000
--- a/man/getOPLSDA.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getOPLSDA.R
-\name{getOPLSDA}
-\alias{getOPLSDA}
-\title{calculate VIP values}
-\usage{
-getOPLSDA(x, Group = NULL)
-}
-\arguments{
-\item{x}{sample ion intensity matrix, row sample, column feature.}
-
-\item{Group}{sample group information}
-}
-\value{
-a dataframe with vip values
-}
-\description{
-calculate VIP values using among different samples groups using OPLSDA.
-}
-\examples{
-dat <- matrix(runif(2*300), ncol = 2, nrow = 300)
-myGroup <- rep_len(LETTERS[1:3], 300)
-out <- getOPLSDA(dat, Group = myGroup)
-}