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

Overrides 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.

neg_log_delta

The negative logarithm of the convergence threshold for the likelihood increase.

outlier_handling

What to do with outliers: - ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem) - none: do nothing

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.)

Workflows

• Labelfree with Protein QuantificationKNIME Hub
• labelfree_with_protein_quantificationOpenMS
• labelfree_with_protein_quantificationKNIME Hub
• Peptide Identification from MSKNIME Hub
• Protein label-free quantificationKNIME Hub
• Show all 9 workflows

Links

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Developers