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This function takes all possible combination of pepfiles of length greater or equal than 2 and computes the number of estimated incorrect petides, the number of unique peptides, the number of unique protetypic peptides and the false discovery rate after merging for each combination. The best combination has an fdr lower than masterFdr and the highest number of unique (proteotypic) peptides.
This function takes a final peptide file and returns information about the unique peptide scores and their number in each peptide matchType (PepFrag1 and PepFrag2) by protein dataBaseType (Random and Regular) category. The function is a lightweight verion of getPepNumbers and plotPepScores (to be used with Synapter instances) for individual files.
This function combines a list of peptide final peptide files into one single master file that is obtained by merging the unique peptides from the filtered original peptide files.
The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.
synergise
(Package: synapter) :
Synergise identification and quantitation results
Performs a complete default analysis on the files defined in filenames, creates a complete html report and saves/exports all results as csv and rda files. See details for a description of the pipeline and Synapter for manual execution of individual steps.
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