SRFilter-class: "SRFilter" for representing functions operating on ShortRead...

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples


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 srFilter function.

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 srFilter page.



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 x satisfying 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.


Class "function", from data part. Class ".SRUtil", directly. Class "OptionalFunction", by class "function", distance 2. Class "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 single FilterRules object.


Martin Morgan <[email protected]>

See Also

srFilter for predefined and user-defined filters.


## see ?srFilter

ShortRead documentation built on Feb. 23, 2018, 2 a.m.