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MapAlignerPoseClustering

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Corrects retention time distortions between maps using a pose clustering approach.

Web Documentation for 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
Overwrite 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))

Input Ports

Input files to align (all must have the same file type) [featureXML,mzML]
File to use as reference (same file format as input files required) [featureXML,mzML,opt.]

Output Ports

Output files (same file type as 'in'). This option or 'trafo_out' has to be provided; they can be used together. [featureXML,mzML]
Transformation output files. This option or 'out' has to be provided; they can be used together. [trafoXML]

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.1
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