(original) (raw)

## ----global_options, include=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- old <- options() options(width = 999) knitr::opts_chunk$set(fig.align='center', fig.width=5.5, fig.height=4.5, message=FALSE) ## ----install, echo=TRUE, eval=FALSE, results='hide'---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # install.packages("https://cran.r-project.org/src/contrib/Archive/MALDIrppa/MALDIrppa\_1.0.5-1.tar.gz", # repo=NULL, type="source") ## ----loading, echo=TRUE, eval=TRUE, results='hide'----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- library(MALDIrppa) ## ----loading2, echo=TRUE, eval=TRUE, results='hide'---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- data(spectra) # list of MassSpectra class objects data(type) # metadata matrix ## ----summary, echo=TRUE, eval=TRUE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- summarySpectra(spectra[1:10]) ## ----iniscreening, echo=TRUE, eval=TRUE, fig.align='center', fig.width=5.5, fig.height=4.5------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- sc.results <- screenSpectra(spectra, meta = type) summary(sc.results) plot(sc.results, labels = TRUE) ## ----spectraplots10, echo=TRUE, eval=TRUE, fig.align='center'------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ plot(spectra[[28]]) plot(spectra[[29]]) plot(spectra[[87]]) ## ----iniscreening3, echo=TRUE, eval=TRUE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- spectra <- sc.results$fspectra # Filtered list of mass spectra type <- sc.results$fmeta # Filtered metadata ## ----parameters, echo=TRUE, eval=TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # Pre-processing parameter settings thScale <- 2.5 # Smoothing ite <- 105 # Baseline correction SigNoi <- 2 # Peak extraction hws <- 20 # Peak extraction tol <- 0.003 # Peak binning ## ----deno, echo=TRUE, eval=TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ spectra <- transfIntensity(spectra, fun = sqrt) spectra <- wavSmoothing(spectra, method = "Wavelet", thresh.scale = thScale) spectra <- removeBaseline(spectra, method = "SNIP", iterations = ite) spectra <- calibrateIntensity(spectra, method = "PQN") ## ----peaks, echo=TRUE, eval=TRUE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- peaks <- detectPeaks(spectra, SNR = SigNoi, halfWindowSize = hws) peaks <- alignPeaks(peaks, minFreq = 0.8, tolerance = tol) ## ----peakssummary, echo=TRUE, eval=TRUE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- summaryPeaks(peaks[1:10]) ## ----npeaks, echo=TRUE, eval=TRUE, fig.align='center'-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- cP <- countPeaks(peaks) plot(cP, type = "n") text(cP, label = 1:length(cP)) ## ----saving, echo=TRUE, eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # save(peaks, file = file.path(tempdir(), "peaks.pp.Rdata")) # save(type, file = file.path(tempdir(), "type.pp.Rdata")) ## ----intmatrix, echo=TRUE, eval=TRUE, fig.align='center'----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- peakPatterns(peaks) ## ----outliers, echo=TRUE, eval=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- out <- detectOutliers(peaks, type$Isolate, binary = TRUE) ## ----outliers2, echo=TRUE, eval=TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- peaks.clean <- peaks[out[,2] == FALSE] # Discard outlying peak profiles type.clean <- type[out[,2] == FALSE,] # and corresponding metadata ## ----filtering, echo=TRUE, eval=TRUE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- peaks.clean.f <- filterPeaks(peaks.clean, minFreq = 0.25, labels = type.clean$Isolate) ## ----intmatrix2, echo=TRUE, eval=TRUE, fig.align='center'---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- peakPatterns(peaks.clean.f) ## ----merge, echo=TRUE, eval=TRUE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- peaks.clean.fm <- mergeMassPeaks(peaks.clean.f, labels = type.clean$Isolate, method = "median") type.clean.fm <- aggregate(type.clean, list(Isolate = type.clean$Isolate), FUN = length)[,1] ## ----finalint, echo=TRUE, eval=TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- int.clean.fm <- intensityMatrix(peaks.clean.fm) ## ----savefinal, echo=TRUE, eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ # writeMetadata(type.clean.fm, file = file.path(tempdir(),"type.clean.fm"), # format = "csv") # save metadata # writeIntensity(int.clean.fm, file = file.path(tempdir(),"int.clean.fm"), # format = "csv", labels = type.clean.fm) # writeIntensity(int.clean.fm, file = file.path(tempdir(),"int.clean.fm"), # format = "NEXUS", labels = type.clean.fm) ## ----global_options_exit, include=FALSE--------------------------------------- options(old)