Transformation products obtained from formula annotations

Source: R/TP-ann_form.R

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

# S4 method for class 'transformationProductsAnnForm'
filter(
  obj,
  ...,
  minFitFormula = 0,
  minTPScore = 0,
  topMost = NULL,
  verbose = TRUE,
  negate = FALSE
)

Arguments

obj

The transformationProductsAnnForm object that should be filtered.

...

Further arguments passed to the parent filter method.

minFitFormula, minTPScore

Thresholds related to TP scoring. See generateTPsAnnForm 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 transformationProductsFormula base class, please see its documentation for more details. Objects from this class are returned by generateTPsAnnForm.

Methods (by generic)

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

S4 class hierarchy

See also

The base class transformationProductsFormula for more relevant methods and generateTPsAnnForm