filter-class: A class for representing filtering operations to be applied...

In flowCore: flowCore: Basic structures for flow cytometry data

Description

The filter class is the virtual base class for all filter/gating objects in flowCore. In general you will want to subclass or create a more specific filter.

Slots

filterId

A character vector that identifies this filter. This is typically user specified but can be automatically deduced by certain filter operations, particularly boolean and set operations.

Objects from the Class

All filter objects in flowCore should be instantiated through their constructors. These are functions that share the same name with the respective filter classes. E.g., rectangleGate() is the constructor function for rectangular gates, and kmeansFilter() creates objects of class kmeansFilter. Usually these constructors can deal with various different inputs, allowing to utilize the same function in different programmatic or interactive settings. For all filters that operate on specific flow parameters (i.e., those inheriting from parameterFilter), the parameters need to be passed to the constructor, either as names or colnames of additional input arguments or explicitly as separate arguments. See the documentation of the respective filter classes for details. If parameters are explicitly defined as separate arguments, they may be of class character, in which case they will be evaluated literally as colnames in a flowFrame, or of class transform, in which case the filtering is performed on a temporarily transformed copy of the input data. See here for details.

Methods

%in%

Used in the usual way this returns a vector of values that identify which events were accepted by the filter. A single filter may encode several populations so this can return either a logical vector, a factor vector or a numeric vector of probabilities that the event is accepted by the filter. Minimally, you must implement this method when creating a new type of filter

&, |, !

Two filters can be composed using the usual boolean operations returning a filter class of a type appropriate for handling the operation. These methods attempt to guess an appropriate filterId for the new filter

%subset%, %&%

Defines a filter as being a subset of another filter. For deterministic filters the results will typically be equivalent to using an \& operation to compose the two filters, though summary methods will use subset semantics when calculating proportions. Additionally, when the filter is data driven, such as norm2Filter, the subset semantics are applied to the data used to fit the filter possibly resulting in quite different, and usually more desirable, results.

%on%

Used in conjunction with a transformList to create a transformFilter. This filter is similar to the subset filter in that the filtering operation takes place on transformed values rather than the original values.

filter

A more formal version of %in%, this method returns a filterResult object that can be used in subsequent filter operations as well as providing more metadata about the results of the filtering operation. See the documenation for filter methods for details.

summarizeFilter

When implementing a new filter this method is used to update the filterDetails slot of a filterResult. It is optional and typically only needs to be implemented for data-driven filters.

Author(s)

B. Ellis, P.D. Haaland and N. LeMeur

See Also

transform, filter

flowCore documentation built on Nov. 8, 2020, 5:19 p.m.