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| ppc.cv | Cross-validation for PPC analysis |
| ppc.fdr | Function to estimate False Discovery rates for peaks in PPC analysis |
| ppc.find.splits | Function to find best discriminating split points for training data in mass spec |
| ppc.make.centroid.list | Function to make a list of peak centroids, from a set of peaks from different spectra |
| ppc.make.peaklist | Function to extract peaks from raw mass spec data |
| ppc.peak.summary | Produce summary of peaks from PPC analysis |
| ppc.peaks | Find local maxima |
| ppc.plot.hist | Plot peak histograms from PPC analysis |
| ppc.plotcv | Function to plot CV curves from PPC analysis |
| ppc.plotcvprob | Function to plot CV probabilities from PPC analysis |
| ppc.plotfdr | Function to plot FDR results from PPC analysis |
| ppc.predict | Function to do test set prediction for the PPC method |
| ppc.predict.peaks | A function to find centroid peaks, in a list of individual peaks |
| ppc.predict.peaks1 | A function to find centroid peaks, in a list of individual peaks from one spectrum |
| ppc.predict1 | Function to do a single test set prediction for the PPC method |
| ppc.read.peaks.batch | Read in mass spec peak data, with batches |
| ppc.read.peaks.nobatch | Read in mass spec peak data, without batches |
| ppc.read.raw.batch | A function to read in raw protein mass spec data, with batches |
| ppc.read.raw.nobatch | A function to read in raw protein mass spec data, with no batches |
| ppc.remove.beforeslash.and.suffix | Remove characters efore a slash and at end |
| ppc.remove.suffix | Function to remove the suffix from a file name |
| ppc.subset.and.reshape | Function to subset and reshape raw mass spec data |
| ppc.subset.and.reshape.peakdata | Function to subset and reshape mass spec peak data |