FeatureLinkerUnlabeledQT

Options

version

Version of the tool that generated this parameters file.

keep_subelements

For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.

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)

use_identifications

Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).

nr_partitions

How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution).

min_nr_diffs_per_bin

If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region. RT regions will be extended until that number is reached.

min_IDscore_forTolCalc

If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation. Check your current score type!

noID_penalty

If IDs are used: For the normalized distances, how high should the penalty for missing IDs be? 0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away).

ignore_charge

false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state

ignore_adduct

true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts

max_difference

Never pair features with a larger RT distance (in seconds).

exponent

Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

weight

Final RT distances are weighted by this factor

max_difference

Never pair features with larger m/z distance (unit defined by 'unit')

unit

Unit of the 'max_difference' parameter

exponent

Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

weight

Final m/z distances are weighted by this factor

exponent

Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

weight

Final intensity distances are weighted by this factor

log_transform

Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))

Views

FeatureLinkerUnlabeledQT Std Output

The text sent to standard out during the execution of FeatureLinkerUnlabeledQT.

FeatureLinkerUnlabeledQT Error Output

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

Workflows

• 02-PIA_and_quantKNIME Hub
• Labelfree with Protein QuantificationKNIME Hub
• labelfree_with_protein_quantificationOpenMS
• labelfree_with_protein_quantificationKNIME Hub
• Metabolite_Adduct_GroupingOpenMS
• Show all 16 workflows

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