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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 |
| coverage | A function to calculate the coverage percentage |
| cv | A function to calculate the CV (Coeffient of Variation) |
| fdr.crit | A function to calculate the number of samples pass fdr threshold |
| getFdrBins | Function to calculate the percentage of fdrs in each bin |
| 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 |
| quantification.accuracy | Measurment of quantification accuracy of two Swath results |
| readLibFile | Load a spectrum library into a data frame |
| reliabilityCheckLibrary | A function to check the coverage of the extended library given the seed library |
| reliabilityCheckSwath | A function to check the coverage, fdr distrubtions, quantification accuary etc of two Swath results |
| swath.means | Computer Swath mean peak area for duplicated samples |