SWATH extended library generation and satistical data analysis


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Documentation for package ‘SwathXtend’ version 1.0.0

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applyttest Utility to apply a t-test to all rows of a matrix
applyttestPep Function to apply t-test separately for all peptides of each protein
buildSpectraLibPair Build a spectra library by integrating a pair of spectrum libraries
canonicalFormat Standardise a sprectrum library data frame
checkQuality Checking for the integration quality of two libraries
cleanLib Spectrum library cleanining
ionCorGS Gold standard relative ion intensity correlation (spearman)
medianNorm Utility to median normalize a matrix by columns
mlr Function to implement mlr normalization
mlrGroup Function to do mlr normalization for a matrix group
mlrrep Function to do mlr normalizatiopn on a matrix of replicates
outputLib output a spectrum library into a PeakView format file
plotAll Plot statistical plots for two libraries
plotDensities Utility to do side by side density plots
plotErrorBarsLines Utility for clustering plots to plot lines and an overall trend
plotRelativeDensities Plotting utility to overlay all relative densities
plotRIICor Plot relative ion intensity correlation of two libraries
plotRTCor Plot for retention time correlation of two libraries
plotRTResd Plot residuals for retention time prediction of two libraries
readLibFile Load a spectrum library into a data frame