Transformation products obtained from compound annotations

Class to store results transformation products (TPs) obtained from compound annotations.

Usage

# S4 method for class 'transformationProductsAnnComp'
filter(
  obj,
  ...,
  minFitFormula = 0,
  minFitCompound = 0,
  minSimSusp = 0,
  minFitCompOrSimSusp = c(0, 0),
  minTPScore = 0,
  topMost = NULL,
  verbose = TRUE,
  negate = FALSE
)

Arguments

obj

The transformationProductsAnnComp object that should be filtered.

...

Further arguments passed to the parent filter method.

minFitFormula, minFitCompound, minSimSusp, minFitCompOrSimSusp, minTPScore

Thresholds related to TP scoring. See generateTPsAnnComp for more details.

topMost

Only keep this number of top-most TPs (based on TPScore) for each parent/feature group combination. Set to NULL to skip this step.

verbose

If set to FALSE then no text output is shown.

negate

If TRUE then filters are performed in opposite manner.

Details

This class is derived from the transformationProductsStructure base class, please see its documentation for more details. Objects from this class are returned by generateTPsAnnComp.

Methods (by generic)

• filter(transformationProductsAnnComp): Performs rule-based filtering. Useful to simplify and clean-up the data.

S4 class hierarchy

• transformationProductsStructure

  • transformationProductsAnnComp

See also

The base class transformationProductsStructure for more relevant methods and generateTPsAnnComp