## ----set, include=FALSE------------------------------------------------------- knitr::opts_chunk$set(fig.width=12, fig.height=8) ## ----eval=FALSE--------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ptairMS") ## ----package, message = FALSE, warning = FALSE-------------------------------- library(ptairMS) library(ptairData) ## ----eval=FALSE--------------------------------------------------------------- # ptairMS::RunShinnyApp() ## ----ptairData---------------------------------------------------------------- dirRaw <- system.file("extdata/exhaledAir", package = "ptairData") ## ----createPtrSet------------------------------------------------------------- exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset", mzCalibRef = c(21.022, 60.0525),fracMaxTIC = 0.7, saveDir = NULL ) ## ----------------------------------------------------------------------------- exhaledPtrset ## ----getFileNames------------------------------------------------------------- getFileNames(exhaledPtrset) ## ----plot--------------------------------------------------------------------- plot(exhaledPtrset) ## ----calib table-------------------------------------------------------------- calib_table<-read.csv(system.file("extdata", "reference_tables/calib_table.tsv", package = "ptairMS"),sep="\t") knitr::kable(calib_table) ## ----calibration-------------------------------------------------------------- plotCalib(exhaledPtrset,fileNames=getFileNames(exhaledPtrset)[1]) ## ----plotCalib---------------------------------------------------------------- exhaledPtrset <- calibration(exhaledPtrset, mzCalibRef = c(21.022, 60.0525,75.04406)) plot(exhaledPtrset,type="calibError") ## ----shinny app, eval=FALSE--------------------------------------------------- # exhaledPtrset <- changeTimeLimits(exhaledPtrset) ## ----timeLimits1-------------------------------------------------------------- samplePath <-getFileNames(exhaledPtrset,fullNames = TRUE)[1] sampleRaw <- readRaw(samplePath, calib = FALSE) expirationLimit <- timeLimits(sampleRaw,fracMaxTIC = 0.5,plotDel = TRUE, mzBreathTracer = 60.05) expirationLimit <- timeLimits(sampleRaw,fracMaxTIC = 0.9,plotDel = TRUE,mzBreathTracer = NULL) ## ----plotTIC1----------------------------------------------------------------- plotTIC(object = exhaledPtrset,baselineRm = TRUE,type = "ggplot") ## ----getSampleMetadata-------------------------------------------------------- getSampleMetadata(exhaledPtrset) ## ----setSampleMetadata-------------------------------------------------------- sampleMD <- getSampleMetadata(exhaledPtrset) colnames(sampleMD)[1] <- "individual" exhaledPtrset <- setSampleMetadata(exhaledPtrset,sampleMD) getSampleMetadata(exhaledPtrset) ## ----exportSampleMetada,eval=FALSE-------------------------------------------- # exportSampleMetada(exhaledPtrset, saveFile = file.path(DirBacteria,"sampleMetadata.tsv")) # exhaledPtrset <- importSampleMetadata(exhaledPtrset, file = file.path(DirBacteria,"sampleMetadata.tsv")) ## ----plotRaw_ptrSet----------------------------------------------------------- plotRaw(exhaledPtrset, mzRange = 59 , fileNames = getFileNames(exhaledPtrset)[1],showVocDB = TRUE) ## ----plotFeatures, message=FALSE, warning=FALSE------------------------------- plotFeatures(exhaledPtrset,mz=59.049,type="ggplot",colorBy = "individual") ## ----update------------------------------------------------------------------- exhaledPtrset <- updatePtrSet(exhaledPtrset) ## ----Detect_peak-------------------------------------------------------------- exhaledPtrset <- detectPeak(exhaledPtrset) ## ----getPeakList-------------------------------------------------------------- peakList<-getPeakList(exhaledPtrset) peakList1<-peakList$`ind1-1.h5` X<-Biobase::exprs(peakList1) Y<-Biobase::fData(peakList1) mz<-Y[,"Mz"] plot(X[which.min(abs(mz-59.0498)),],ylab="cps",xlab="time",main=paste("Temporal evolution of acetone ")) head(Y) ## ----updatePtrSet,eval=FALSE-------------------------------------------------- # exhaledPtrset<-updatePtrSet(exhaledPtrset) # exhaledPtrset<-setSampleMetadata(exhaledPtrset,resetSampleMetadata(exhaledPtrset)) # exhaledPtrset<-detectPeak(exhaledPtrset) ## ----Align patient------------------------------------------------------------ exhaledEset <- alignSamples(exhaledPtrset, group="individual", fracGroup = 1, fracExp=1/6) ## ----------------------------------------------------------------------------- knitr::kable(head(Biobase::exprs(exhaledEset))) knitr::kable(head(Biobase::pData(exhaledEset))) knitr::kable(head(Biobase::fData(exhaledEset))) ## ----impute------------------------------------------------------------------- exhaledEset <- ptairMS::impute(exhaledEset, exhaledPtrset) ## ----------------------------------------------------------------------------- annotateVOC(59.049) exhaledEset<-annotateVOC(exhaledEset) knitr::kable(head(Biobase::fData(exhaledEset))) ## ----eval=FALSE--------------------------------------------------------------- # writeEset(exhaledEset, dirC = file.path(getwd(), "processed_dataset")) ## ----log_transform------------------------------------------------------------ Biobase::exprs(exhaledEset) <- log2(Biobase::exprs(exhaledEset)) ## ----view--------------------------------------------------------------------- ropls::view(Biobase::exprs(exhaledEset),printL=FALSE) ## ----discarding isotopes------------------------------------------------------ isotopes<-Biobase::fData(exhaledEset)[,"isotope"] isotopes<-isotopes[!is.na(isotopes)] exhaledEset <- exhaledEset[!(Biobase::fData(exhaledEset)[, "ion_mass"] %in% isotopes), ] ## ----pca---------------------------------------------------------------------- exhaledPca<-ropls::opls(exhaledEset,crossvalI=5,info.txtC="none",fig.pdfC="none") ropls::plot(exhaledPca, parAsColFcVn=Biobase::pData(exhaledEset)[, "individual"],typeVc="x-score") ## ----------------------------------------------------------------------------- load1<-ropls::getLoadingMN(exhaledPca)[,1] barplot(sort(abs(load1),decreasing = TRUE)) knitr::kable(Biobase::fData(exhaledEset)[names(sort(abs(load1),decreasing = TRUE)[1:10]),c("vocDB_ion_formula","vocDB_name_iupac")]) ## ----plotFeatures individual, warning=FALSE----------------------------------- plotFeatures(exhaledPtrset,mz = 53.0387,typePlot = "ggplot",colorBy = "individual") plotFeatures(exhaledPtrset,mz = 67.0539,typePlot = "ggplot",colorBy = "individual") ## ----------------------------------------------------------------------------- dir <- system.file("extdata/mycobacteria", package = "ptairData") mycobacteriaSet <- createPtrSet(dir = dir, setName = "test", mzCalibRef = c(21.022,59.049)) mycobacteriaSet <- detectPeak(mycobacteriaSet, smoothPenalty = 0) plotTIC(mycobacteriaSet,type="ggplot",showLimits = TRUE,file="Specie-a2.h5") eSet <- alignSamples(mycobacteriaSet) eSet<-impute(eSet,ptrSet = mycobacteriaSet) X<-Biobase::exprs(eSet) pca<-ropls::opls(log2(t(X)),predI =2,crossvalI=5,info.txtC = "none", fig.pdfC = "none") ropls::view(log2(X),printL=FALSE) plot(pca,type="x-score") ## ----readRaw------------------------------------------------------------------ dirRaw <- system.file("extdata/exhaledAir", package = "ptairData") samplePath<-list.files(dirRaw,recursive = TRUE,full.names = TRUE,pattern = ".h5$")[1] ## ----------------------------------------------------------------------------- sampleRaw <- readRaw(samplePath, calib = FALSE) sampleRaw ## ----sessionInfo-------------------------------------------------------------- sessionInfo()