SRFilterResult-class: "SRFilterResult" for SRFilter output and statistics

In Bioconductor/ShortRead: FASTQ input and manipulation

"SRFilterResult" for SRFilter output and statistics

Description

Objects of this class are logical vectors indicating records passing the applied filter, with an associated data frame summarizing the name, input number of records, records passing filter, and logical operation used for all filters in which the result participated.

Usage

SRFilterResult(x = logical(), name = NA_character_,
   input = length(x), passing = sum(x), op = NA_character_)
## S4 method for signature 'SRFilterResult,SRFilterResult'
Logic(e1, e2)
## S4 method for signature 'SRFilterResult'
name(x, ...)
stats(x, ...)
## S4 method for signature 'SRFilterResult'
show(object)

Arguments

x, object, e1, e2	For SRFilterResult, logical() indicating records that passed filter or, for others, an instance of SRFilterResult class.
name	character() indicating the name by which the filter is to be referred. Internally, name, input, passing, and op may all be vectors representing columns of a data.frame summarizing the application of successive filters.
input	integer() indicating the length of the original input.
passing	integer() indicating the number of records passing the filter.
op	character() indicating the logical operation, if any, associated with this filter.
...	Additional arguments, unused in methods documented on this page.

Objects from the Class

Objects can be created through SRFilterResult, but these are automatically created by the application of srFilter instances.

Slots

.Data:

Object of class "logical" indicating records that passed the filter.

name:

Object of class "ScalarCharacter" representing the name of the filter whose results are summarized. The name is either the actual name of the filter, or a combination of filter names and logical operations when the outcome results from application of several filters in a single logical expression.

stats:

Object of class "data.frame" summarizing the name, input number of records, records passing filter, and logical operation used for all filters in which the result participated. The data.frame rows correspond either to single filters, or to logical combinations of filters.

Extends

Class "logical", from data part. Class ".SRUtil", directly. Class "vector", by class "logical", distance 2. Class "atomic", by class "logical", distance 2. Class "vectorORfactor", by class "logical", distance 3.

Methods

Logic

signature(e1 = "SRFilterResult", e2 = "SRFilterResult"): logic operations on filters.

!

signature(x = "SRFilterResult"): Negate the outcome of the current filter results

name

signature(x = "SRFilterResult"): The name of the filter that the results are based on.

stats

signature(x = "SRFilterResult"): a data.frame as described in the ‘Slots’ section of this page.

show

signature(object = "SRFilterResult"): summary of filter results.

Author(s)

Martin Morgan mailto:[e-mail]

See Also

srFilter

Examples

fa <- srFilter(function(x) x %% 2 == 0, "Even")
fb <- srFilter(function(x) x %% 2 == 1, "Odd")

x <- 1:10
fa(x) | fb(x)
fa(x) & fb(x)
!(fa(x) & fb(x))

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