Nothing
## ----setup, include=FALSE, cache=FALSE----------------------------------------
library("knitr")
opts_chunk$set(tidy.opts=list(width.cutoff=45), tidy=FALSE, fig.align="center",
fig.height=4.25, comment=NA, prompt=TRUE)
## ----env, echo=FALSE----------------------------------------------------------
suppressPackageStartupMessages(library("MALDIquant"))
## ----mqsetup, eval=FALSE------------------------------------------------------
# install.packages(c("MALDIquant", "MALDIquantForeign"))
## ----mqlibrary, eval=FALSE----------------------------------------------------
# library("MALDIquant")
## ----mqobjects----------------------------------------------------------------
s <- createMassSpectrum(mass=1:10, intensity=1:10,
metaData=list(name="Spectrum1"))
s
## ----mqaccess-----------------------------------------------------------------
mass(s)
intensity(s)
metaData(s)
## ----mqdataimport-------------------------------------------------------------
data(fiedler2009subset)
## ----mqdataimport2------------------------------------------------------------
length(fiedler2009subset)
fiedler2009subset[1:2]
## ----mqqclength---------------------------------------------------------------
any(sapply(fiedler2009subset, isEmpty))
table(sapply(fiedler2009subset, length))
## ----mqqcregular--------------------------------------------------------------
all(sapply(fiedler2009subset, isRegular))
## ----mqqcplots----------------------------------------------------------------
plot(fiedler2009subset[[1]])
plot(fiedler2009subset[[16]])
## ----mqvs---------------------------------------------------------------------
spectra <- transformIntensity(fiedler2009subset,
method="sqrt")
## ----mqsm---------------------------------------------------------------------
spectra <- smoothIntensity(spectra, method="SavitzkyGolay",
halfWindowSize=10)
## ----mqve---------------------------------------------------------------------
baseline <- estimateBaseline(spectra[[16]], method="SNIP",
iterations=100)
plot(spectra[[16]])
lines(baseline, col="red", lwd=2)
## ----mqbc---------------------------------------------------------------------
spectra <- removeBaseline(spectra, method="SNIP",
iterations=100)
plot(spectra[[1]])
## ----mqcb---------------------------------------------------------------------
spectra <- calibrateIntensity(spectra, method="TIC")
## ----mqpa---------------------------------------------------------------------
spectra <- alignSpectra(spectra,
halfWindowSize=20,
SNR=2,
tolerance=0.002,
warpingMethod="lowess")
## ----mqav1--------------------------------------------------------------------
samples <- factor(sapply(spectra,
function(x)metaData(x)$sampleName))
## ----mqav2--------------------------------------------------------------------
avgSpectra <- averageMassSpectra(spectra, labels=samples,
method="mean")
## ----mqpd1--------------------------------------------------------------------
noise <- estimateNoise(avgSpectra[[1]])
plot(avgSpectra[[1]], xlim=c(4000, 5000), ylim=c(0, 0.002))
lines(noise, col="red")
lines(noise[,1], noise[, 2]*2, col="blue")
## ----mqpd2--------------------------------------------------------------------
peaks <- detectPeaks(avgSpectra, method="MAD",
halfWindowSize=20, SNR=2)
plot(avgSpectra[[1]], xlim=c(4000, 5000), ylim=c(0, 0.002))
points(peaks[[1]], col="red", pch=4)
## ----mqpb---------------------------------------------------------------------
peaks <- binPeaks(peaks, tolerance=0.002)
## ----mqfp---------------------------------------------------------------------
peaks <- filterPeaks(peaks, minFrequency=0.25)
## ----mqim---------------------------------------------------------------------
featureMatrix <- intensityMatrix(peaks, avgSpectra)
head(featureMatrix[, 1:3])
## ----sessioninfo, echo=FALSE, results="asis"----------------------------------
toLatex(sessionInfo(), locale=FALSE)
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