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

In Bioconductor/ShortRead: FASTQ input and manipulation

"SRFilter" for representing functions operating on ShortRead objects

Description

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.

Slots

.Data:

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.

name:

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.

Extends

Class "function", from data part. Class ".SRUtil", directly. Class "OptionalFunction", by class "function", distance 2. Class "PossibleMethod", by class "function", distance 2.

Methods

srFilter

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

name

signature(x = "SRFilter"): Return, as a ScalarCharacter, the name of the function.

show

signature(object = "SRFilter"): display a brief summary of the filter

coerce

signature(from = "SRFilter", to = "FilterRules"): Coerce a filter to a FilterRules object of length one.

c

signature(x = "SRFilter", ...): Combine filters into a single FilterRules object.

Author(s)

Martin Morgan <[e-mail]>

See Also

srFilter for predefined and user-defined filters.

Examples

## see ?srFilter

Bioconductor/ShortRead documentation built on Nov. 2, 2024, 4:38 p.m.