Man pages for SwathXtend
SWATH extended library generation and statistical data analysis

applyttestUtility to apply a t-test to all rows of a matrix
applyttestPepFunction to apply t-test separately for all peptides of each...
buildSpectraLibPairBuild a spectra library by integrating a pair of spectrum...
canonicalFormatStandardise a sprectrum library data frame
checkQualityChecking for the integration quality of two libraries
cleanLibSpectrum library cleanining
coverageA function to calculate the coverage percentage
cvA function to calculate the CV (Coeffient of Variation)
fdr.critA function to calculate the number of samples pass fdr...
getFdrBinsFunction to calculate the percentage of fdrs in each bin
ionCorGSGold standard relative ion intensity correlation (spearman)
medianNormUtility to median normalize a matrix by columns
mlrFunction to implement mlr normalization
mlrGroupFunction to do mlr normalization for a matrix group
mlrrepFunction to do mlr normalizatiopn on a matrix of replicates
outputLiboutput a spectrum library into a PeakView format file
plotAllPlot statistical plots for two libraries
plotDensitiesUtility to do side by side density plots
plotErrorBarsLinesUtility for clustering plots to plot lines and an overall...
plotRelativeDensitiesPlotting utility to overlay all relative densities
plotRIICorPlot relative ion intensity correlation of two libraries
plotRTCorPlot for retention time correlation of two libraries
plotRTResdPlot residuals for retention time prediction of two libraries
quantification.accuracyMeasurment of quantification accuracy of two Swath results
readLibFileLoad a spectrum library into a data frame
reliabilityCheckLibraryA function to check the coverage of the extended library...
reliabilityCheckSwathA function to check the coverage, fdr distrubtions,...
swath.meansComputer Swath mean peak area for duplicated samples
SwathXtend documentation built on Oct. 31, 2019, 5:38 a.m.