SWATH extended library generation and satistical data analysis

Documentation for package ‘SwathXtend’ version 1.4.0

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