update contam() and getMax() functions

.gitignore

@@ -1,5 +1,6 @@
 .Rproj.user
 .Rhistory
 .RData
+.RDataTmp
 .Ruserdata
 .Rbuildignore

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)

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!")}

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)

R/getSname.R → 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");
 }