"SRFilter" for representing functions operating on ShortRead objects
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 from the Class
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
xcorresponding 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
xto include those elements of
xsatisfying the filter.
Object of class
"ScalarCharacter"representing the name of the filter. The name is useful for suggesting the purpose of the filter, and for debugging failed filters.
"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
FilterRulesobject of length one.
signature(x = "SRFilter", ...): Combine filters into a single
Martin Morgan <firstname.lastname@example.org>
srFilter for predefined and user-defined filters.
## see ?srFilter
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