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

Overrides 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.

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.)

Workflows

• KNIME_GNPSExportKNIME Hub
• MHCquantKNIME Hub

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