FalseDiscoveryRate

Options

version

Version of the tool that generated this parameters file.

PSM

Perform FDR calculation on PSM level

peptide

Perform FDR calculation on peptide level and annotates it as meta value (Note: if set, also calculates FDR/q-value 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

Overrides 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)

remove_proteins_without_psms

Remove proteins without PSMs (due to being decoy or below PSM FDR threshold).

remove_psms_without_proteins

Remove PSMs without proteins (due to being decoy or below protein FDR threshold).

remove_spectra_without_psms

Remove spectra without PSMs (due to being decoy or below protein FDR threshold). Caution: if remove_psms_without_proteins is false, protein level filtering does not propagate.

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.

conservative

If 'true' (D+1)/T instead of (D+1)/(T+D) is used as a formula.

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.)

Workflows

• 01-MaCProQCKNIME Hub
• 02-download_and_analyze_raw_fileKNIME Hub
• basic_peptide_identificationKNIME Hub
• basic_peptide_identification_with_inferenceKNIME Hub
• basic_peptide_identification_with_inferenceKNIME Hub
• Show all 27 workflows

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Developers