Objects of this class are functions that, when provided an appropriate object from the ShortRead package, return logical vectors indicating which parts of the object satisfy the filter criterion.
A number of filters are built-in (described below); users are free to
create their own filters, using the
Objects can be created through
srFilter (to create a
user-defined filter) or through calls to constructors for predefined
filters, as described on the
Object of class
"function" taking a
single named argument
x corresponding to the ShortRead
object that the filter will be applied to. The return value of the
filter function is expected to be a logical vector that can be
used to subset
x to include those elements of
satisfying the filter.
Object of class
representing the name of the filter. The name is useful for
suggesting the purpose of the filter, and for debugging failed
"function", from data part.
"OptionalFunction", by class "function", distance 2.
"PossibleMethod", by class "function", distance 2.
signature(fun = "SRFilter"): Return the function
representing the underlying filter; this is primarily for
interactive use to understanding filter function; usually the
filter is invoked as a normal function call, as illustrated below
signature(x = "SRFilter"): Return, as a
ScalarCharacter, the name of the function.
signature(object = "SRFilter"): display a brief
summary of the filter
signature(from = "SRFilter", to =
"FilterRules"): Coerce a filter to a
FilterRules object of length one.
signature(x = "SRFilter", ...): Combine filters into a
Martin Morgan <firstname.lastname@example.org>
srFilter for predefined and user-defined filters.
## see ?srFilter