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FeatureLinkerUnlabeledKD

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

Groups corresponding features from multiple maps.

Web Documentation for FeatureLinkerUnlabeledKD

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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
mz_unit
Unit of m/z tolerance
nr_partitions
Number of partitions in m/z space
enabled
Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)
rt_tol
Width of RT tolerance window (sec)
mz_tol
m/z tolerance (in ppm or Da)
max_pairwise_log_fc
Maximum absolute log10 fold change between two compatible signals during compatibility graph construction. Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value < 0 disables the FC check.
min_rel_cc_size
Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function
max_nr_conflicts
Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)
rt_tol
Width of RT tolerance window (sec)
mz_tol
m/z tolerance (in ppm or Da)
charge_merging
whether to disallow charge mismatches (Identical), allow to link charge zero (i.e., unknown charge state) with every charge state, or disregard charges (Any).
adduct_merging
whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any).
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
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))
span
Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.
num_iterations
Number of robustifying iterations for lowess fitting.
delta
Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.
interpolation_type
Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation
extrapolation_type
Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.

Input Ports

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input files separated by blanks [featureXML,consensusXML]
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input file containing the experimental design [tsv,opt.]

Output Ports

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Output file [consensusXML]

Views

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

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Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.2
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