IconIDPosteriorErrorProbability0 ×

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.

Web Documentation for IDPosteriorErrorProbability

Options

version
Version of the tool that generated this parameters file.
split_charge
The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed.
top_hits_only
If set only the top hits of every PeptideIdentification will be used
fdr_for_targets_smaller
Only used, when top_hits_only set. Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run.
ignore_bad_data
If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through.
prob_correct
If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications.
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)
number_of_bins
Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized
incorrectly_assigned
for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used.
max_nr_iterations
Bounds the number of iterations for the EM algorithm when convergence is slow.

Input Ports

input file [idXML]

Output Ports

output file [idXML]
txt file (if gnuplot is available, a corresponding PDF will be created as well.) [txt,Inactive]

Views

IDPosteriorErrorProbability Std Output
The text sent to standard out during the execution of IDPosteriorErrorProbability.
IDPosteriorErrorProbability Error Output
The text sent to standard error during the execution of IDPosteriorErrorProbability. (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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Workflows

Update Site

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

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