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FalseDiscoveryRate

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261315 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Estimates the false discovery rate on peptide and protein level using decoy searches.

Web Documentation for FalseDiscoveryRate

Options

version
Version of the tool that generated this parameters file.
PSM
Perform FDR calculation on PSM level
protein
Perform FDR calculation on protein level
log
Name of log file (created only when specified)
debug
Sets the debug level
threads
Sets the number of threads allowed to be used by the TOPP tool
no_progress
Disables progress logging to command line
force
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
PSM
Filter PSMs based on q-value (e.g., 0.05 = 5% FDR, disabled for 1)
protein
Filter proteins based on q-value (e.g., 0.05 = 5% FDR, disabled for 1)
no_qvalues
If 'true' strict FDRs will be calculated instead of q-values (the default)
use_all_hits
If 'true' not only the first hit, but all are used (peptides only)
split_charge_variants
If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only).
treat_runs_separately
If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only).
add_decoy_peptides
If 'true' decoy peptides will be written to output file, too. The q-value is set to the closest target score.
add_decoy_proteins
If 'true' decoy proteins will be written to output file, too. The q-value is set to the closest target score.

Input Ports

Identifications from searching a target-decoy database. [idXML]

Output Ports

Identifications with annotated FDR [idXML]

Views

FalseDiscoveryRate Std Output
The text sent to standard out during the execution of FalseDiscoveryRate.
FalseDiscoveryRate Error Output
The text sent to standard error during the execution of FalseDiscoveryRate. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

KNIME 4.0
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