filter-class {flowCore} | R Documentation |
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.
filterId
:filter
. This is typically user specified but can be
automatically deduced by certain filter operations, particularly
boolean and set operations.
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 explicitely as separate arguments. See
the documentation of the respective filter
classes for
details. If parameters are explicitely defined as separate arguments,
they may be of class character
, in which case they will be
evaluated literaly 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.
%in%
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&
, |
, !
filter
class
of a type appropriate for handling the operation. These methods
attempt to guess an appropriate filterId
for the new
filter
%subset%
, %\&%
\&
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%
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
%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 operationsummarizeFilter
filterDetails
slot of a
filterResult
. It is optional and typically only needs to be
implemented for data-driven filters.
B. Ellis, P.D. Haaland and N. LeMeur