It contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data.
|Author||J WU and D Pascovici|
|Date of publication||None|
|Maintainer||Jemma Wu <firstname.lastname@example.org>|
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...
buildSpectraLibPair: Build a spectra library by integrating a pair of spectrum...
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...
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