From a05dd47343c9bc8d9d5c6e61ce47903b0af74aab Mon Sep 17 00:00:00 2001
From: YonghuiDong <yonghui.dong@gmail.com>
Date: Mon, 8 Feb 2021 14:33:15 +0200
Subject: [PATCH] update contam() and getMax() functions

---
 .gitignore                     |  1 +
 NAMESPACE                      |  2 +-
 R/contaminant.R                |  2 +-
 R/doStat.R                     |  2 +-
 R/{getSname.R => getMax.R}     | 11 +++++++----
 man/contam.Rd                  |  6 +++---
 man/{getSname.Rd => getMax.Rd} | 10 +++++-----
 7 files changed, 19 insertions(+), 15 deletions(-)
 rename R/{getSname.R => getMax.R} (78%)
 rename man/{getSname.Rd => getMax.Rd} (79%)

diff --git a/.gitignore b/.gitignore
index f732fe3..a3116e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 .Rproj.user
 .Rhistory
 .RData
+.RDataTmp
 .Ruserdata
 .Rbuildignore
diff --git a/NAMESPACE b/NAMESPACE
index 68c2352..9cdf479 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,9 +10,9 @@ export(doNormalization)
 export(doStat)
 export(getCV)
 export(getFC)
+export(getMax)
 export(getOPLSDA)
 export(getP)
-export(getSname)
 export(mass)
 export(mz)
 export(ppm)
diff --git a/R/contaminant.R b/R/contaminant.R
index 4e094f2..4d90df5 100644
--- a/R/contaminant.R
+++ b/R/contaminant.R
@@ -9,7 +9,7 @@
 #'  contam(33.0335, ppm = 10, mode = '+')
 #'  contam(44.998, ppm = 10, mode = '-')
 
-contam <- function (mz, ppm = 10, mode = c('+', '-')) {
+contam <- function (mz, mode = NULL, ppm = 10) {
 
   ##(1) input check
   if(is.numeric(mz) == FALSE) {stop("Warning: mass to charge ratio mz shoule be numeric!")}
diff --git a/R/doStat.R b/R/doStat.R
index 1cc9b97..a9a730b 100644
--- a/R/doStat.R
+++ b/R/doStat.R
@@ -12,7 +12,7 @@
 
 doStat <- function(x, Group = NULL){
   cat("\nPerforming statistics: \n")
-  maxSample <- getSname(x)
+  maxSample <- getMax(x)
   myCV <- getCV(x, Group = Group)
   myFC <- getFC(x, Group = Group)
   myP <- getP(x, Group = Group)
diff --git a/R/getSname.R b/R/getMax.R
similarity index 78%
rename from R/getSname.R
rename to R/getMax.R
index b2bd8b4..99e5977 100644
--- a/R/getSname.R
+++ b/R/getMax.R
@@ -6,18 +6,21 @@
 #' @examples
 #' dat <- cbind.data.frame(mz = c(100, 101, 300), mz2 = c(0, 0 , 1), mz3 = c(1, 9, 1))
 #' rownames(dat) <- c("A", "B", "C")
-#' out <- getSname(dat)
+#' out <- getMax(dat)
 
-getSname <- function(x){
+getMax <- function(x){
   cat("\n- Geting sample name with max intensity...\n")
-  ## get the sample name which has the max intensity of each m/z.
+  ## get the sample name which has the max intensity of each m/z
+  ## get the max peak intensity/area
   ## It is useful for further manual identification
   tmp <- t(x)
   if(is.null(colnames(tmp))) stop("No sample names found")
   sample_index <- as.matrix(apply(tmp, 1, which.max))
   sample_index <- as.vector(sample_index, mode = "numeric")
   sample_name <- colnames(tmp)[sample_index]
-  return(sample_name)
+  max_Int <- apply(tmp, 1, max)
+  max_Result <- cbind.data.frame(maxSample = sample_name, maxInt = max_Int)
+  return(max_Result)
   cat("done");
 }
 
diff --git a/man/contam.Rd b/man/contam.Rd
index 547da89..536d718 100644
--- a/man/contam.Rd
+++ b/man/contam.Rd
@@ -4,14 +4,14 @@
 \alias{contam}
 \title{Contaminants in MS}
 \usage{
-contam(mz, ppm = 10, mode = c("+", "-"))
+contam(mz, mode = NULL, ppm = 10)
 }
 \arguments{
 \item{mz}{suspected m/z value}
 
-\item{ppm}{mass tolerance, default value = 10}
-
 \item{mode}{ionization mode, either positive '+' or negative '-'}
+
+\item{ppm}{mass tolerance, default value = 10}
 }
 \description{
 check the possible contaminants
diff --git a/man/getSname.Rd b/man/getMax.Rd
similarity index 79%
rename from man/getSname.Rd
rename to man/getMax.Rd
index ddfc2f4..11928f9 100644
--- a/man/getSname.Rd
+++ b/man/getMax.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getSname.R
-\name{getSname}
-\alias{getSname}
+% Please edit documentation in R/getMax.R
+\name{getMax}
+\alias{getMax}
 \title{Get the sample name which has the max ion intensity}
 \usage{
-getSname(x)
+getMax(x)
 }
 \arguments{
 \item{x}{sample ion intensity matrix, row sample, column feature.}
@@ -18,5 +18,5 @@ get the sample name which has the max ion intensity
 \examples{
 dat <- cbind.data.frame(mz = c(100, 101, 300), mz2 = c(0, 0 , 1), mz3 = c(1, 9, 1))
 rownames(dat) <- c("A", "B", "C")
-out <- getSname(dat)
+out <- getMax(dat)
 }