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FalseDiscoveryRate

Tool to estimate the false discovery rate on peptide and protein level

pot. predecessor tools $ \longrightarrow $ FalseDiscoveryRate $ \longrightarrow $ pot. successor tools
MascotAdapter (or other ID engines) IDFilter
PeptideIndexer

This TOPP tool calculates the false discovery rate (FDR) for results of target-decoy searches. It can handle separate searches of a target database (e.g. forward sequences) and a decoy database (e.g. reversed sequences), or a combined search of a concatenated target-decoy database. The FDR calculation can be performed for proteins and/or for peptides (more exactly, peptide spectrum matches).

The false discovery rate is defined as the number of false discoveries (decoy hits) divided by the number of false and correct discoveries (both target and decoy hits) with a score better than a given threshold.

When using a combined database of target and decoy sequences (thus only running one search per ID engine), PeptideIndexer must be applied to the search results (idXML file) to index the data and to annotate peptide and protein hits with their target/decoy status.

Note
When no decoy hits were found you will get a warning like this:
"FalseDiscoveryRate: #decoy sequences is zero! Setting all target sequences to q-value/FDR 0!"
This should be a serious concern, since it indicates a possible problem with the target/decoy annotation step (PeptideIndexer), e.g. due to a misconfigured database.
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Jan 27 2016 17:15:21 using doxygen 1.8.10