inst/doc/MALDIrppa_vignette_v105.R

In MALDIrppa: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis

## ----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)