MapAlignerPoseClustering

Options

version

Version of the tool that generated this parameters file.

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)

index

Use one of the input files as reference ('1' for the first file, etc.). If '0', no explicit reference is set - the algorithm will select a reference.

max_num_peaks_considered

The maximal number of peaks/features to be considered per map. To use all, set to '-1'.

mz_pair_max_distance

Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.

rt_pair_distance_fraction

Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).

num_used_points

Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.

scaling_bucket_size

The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.

shift_bucket_size

The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans.

max_shift

Maximal shift which is considered during histogramming (in seconds). This applies for both directions.

max_scaling

Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this.

dump_buckets

[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically.

dump_pairs

[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically.

second_nearest_gap

Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.

use_identifications

Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).

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

MapAlignerPoseClustering Std Output

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

MapAlignerPoseClustering Error Output

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

Workflows

• ConsensusXMLIdentificaitonSplitterKNIME Hub
• KNIME_GNPSExportKNIME Hub
• Labelfree with Protein QuantificationKNIME Hub
• labelfree_with_protein_quantificationOpenMS
• labelfree_with_protein_quantificationKNIME Hub
• Show all 17 workflows

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Developers