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 |