## ----style, eval=TRUE, echo=FALSE, results='asis'------------------------
BiocStyle::latex()

## ----env, echo=FALSE,warning=FALSE,message=FALSE-------------------------
suppressPackageStartupMessages(library("metaX"))
#suppressPackageStartupMessages(library("R.utils"))

## ----samList, eval=TRUE--------------------------------------------------
sampleListFile <- system.file("extdata/faahKO_sampleList.txt", 
                              package = "metaX")
samList <- read.delim(sampleListFile)
print(samList)

## ----exampleDir, eval=TRUE-----------------------------------------------
list.files(system.file("cdf", package = "faahKO"),
           recursive = TRUE,full.names = TRUE)

## ----msFilePath, eval=TRUE-----------------------------------------------
## create a metaXpara-class object
#library("metaX")
para <- new("metaXpara")
## set the MS data path
dir.case(para) <- system.file("cdf/KO", package = "faahKO")
dir.ctrl(para) <- system.file("cdf/WT", package = "faahKO")

## set the sample list file path
sampleListFile(para) <- sampleListFile

## ----setParameter,eval=TRUE----------------------------------------------
## set parameters for peak picking
xcmsSet.peakwidth(para) <- c(20,50)
xcmsSet.snthresh(para) <- 10
xcmsSet.prefilter(para) <- c(3,100)
xcmsSet.noise(para) <- 0
xcmsSet.nSlaves(para) <- 4

## ----missValueImputeMethod1,eval=TRUE------------------------------------
## bpca, svdImpute, knn, rf
missValueImputeMethod(para) <- "knn"

## ----missValueImputeMethod2,eval=TRUE------------------------------------
## bpca, svdImpute, knn, rf
missValueImputeMethod(para) <- "knn"

## ----ratioPairs,eval=TRUE------------------------------------------------
## set the comparison groups
ratioPairs(para) <- "KO:WT"

## ----output,eval=TRUE----------------------------------------------------
## set the output parameters
outdir(para) <- "test"
prefix(para) <- "metaX"

## ----rawPeaks,eval=TRUE,echo=FALSE,results='hide',warning=FALSE,message=FALSE----
library(faahKO)
xset <- group(faahko)
xset <- retcor(xset)
xset <- group(xset)
xset <- fillPeaks(xset)
peaksData <- as.data.frame(groupval(xset,"medret",value="into"))
peaksData$name <- row.names(peaksData)
rawPeaks(para) <- peaksData

## ----metaXpipe,eval=FALSE,warning=FALSE,message=FALSE--------------------
## plsdaPara <- new("plsDAPara")
## res <- metaXpipe(para = para,plsdaPara = plsdaPara,
##                cvFilter = 0.2, remveOutlier = TRUE)

## ----sessioninfo, results='asis', echo=FALSE-----------------------------
toLatex(sessionInfo())