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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 can calculate the false discovery rate (FDR) given a forward and backward search (or one run on a combined database). Most useful is this on protein level, however, it also can be applied to peptides.

The false discovery rate is defined as the number of false discoveries (the hits in the reversed search) over the number of false and correct discoveries (the hits in both databases) with a score better than a given threshold.

Prerequisites:

When no decoy hits were found you will get a warning saying something like:
"FalseDiscoveryRate: #decoy sequences is zero! Setting all target sequences to q-value/FDR 0!"
This should be a serious concern, since the target/decoy annotation in a previous step has probably a misconfigured database (see PeptideIndexer).

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 1.11.1 Documentation generated on Mon Dec 23 2013 22:47:51 using doxygen 1.8.5