start: The start(), end(), width(), and pos() generic getters and...

In BiocGenerics: S4 generic functions used in Bioconductor

Description

Get or set the start, end, width, or single positions stored in an object.

NOTE: This man page is for the start, `start<-`, end, `end<-`, width, `width<-`, and pos S4 generic functions defined in the BiocGenerics package. See ?stats::start for the start and end S3 generics defined in the stats package.

Usage

start(x, ...)
start(x, ...) <- value

end(x, ...)
end(x, ...) <- value

width(x)
width(x, ...) <- value

pos(x)

Arguments

x	For the start(), end(), and width() getters/setters: an object containing start, end, and width values. For the pos{} getter: an object containing single positions.
...	Additional arguments, for use in specific methods.
value	The start, end, or width values to set on x.

Value

See specific methods defined in Bioconductor packages.

See Also

• stats::start in the stats package for the start and end S3 generics.

• showMethods for displaying a summary of the methods defined for a given generic function.

• selectMethod for getting the definition of a specific method.

• start,IRanges-method in the IRanges package for examples of specific start, end, and width methods (defined for IRanges objects).

• pos,UnstitchedIPos-method in the IRanges package for an example of a specific pos method (defined for UnstitchedIPos objects).

• BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

## start() getter:
start
showMethods("start")

library(IRanges)
showMethods("start")
selectMethod("start", "IRanges")  # start() getter for IRanges objects

## start() setter:
`start<-`
showMethods("start<-")
selectMethod("start<-", "IRanges")  # start() setter for IRanges objects

## end() getter:
end
showMethods("end")
selectMethod("end", "IRanges")  # end() getter for IRanges objects

## end() setter:
`end<-`
showMethods("end<-")
selectMethod("end<-", "IRanges")  # end() setter for IRanges objects

## width() getter:
width
showMethods("width")
selectMethod("width", "IRanges")  # width() getter for IRanges objects

## width() setter:
`width<-`
showMethods("width<-")
selectMethod("width<-", "IRanges")  # width() setter for IRanges objects

## pos() getter:
pos
showMethods("pos")
selectMethod("pos", "UnstitchedIPos")  # pos() getter for UnstitchedIPos
                                       # objects

Example output

Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

standardGeneric for "start" defined from package "stats"

function (x, ...) 
standardGeneric("start")
<environment: 0x56213133e130>
Methods may be defined for arguments: x
Use  showMethods("start")  for currently available ones.
Function: start (package stats)
x="ANY"

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Function: start (package stats)
x="ANY"
x="CompressedRangesList"
x="IRanges"
x="NCList"
x="NCLists"
x="PartitioningByEnd"
x="PartitioningByWidth"
x="Pos"
x="Ranges"
x="RangesList"
x="Rle"
x="SimpleViewsList"
x="Views"

Method Definition:

function (x, ...) 
x@start
<bytecode: 0x562133f27970>
<environment: namespace:IRanges>

Signatures:
        x        
target  "IRanges"
defined "IRanges"
standardGeneric for "start<-" defined from package "BiocGenerics"

function (x, ..., value) 
standardGeneric("start<-")
<bytecode: 0x562131398df8>
<environment: 0x562131398480>
Methods may be defined for arguments: x
Use  showMethods("start<-")  for currently available ones.
Function: start<- (package BiocGenerics)
x="IntegerRangesList"
x="IRanges"
x="Views"

Method Definition:

function (x, ..., value) 
.set_IRanges_start(x, value)
<bytecode: 0x562133eaadd8>
<environment: namespace:IRanges>

Signatures:
        x        
target  "IRanges"
defined "IRanges"
standardGeneric for "end" defined from package "stats"

function (x, ...) 
standardGeneric("end")
<environment: 0x56212e56b938>
Methods may be defined for arguments: x
Use  showMethods("end")  for currently available ones.
Function: end (package stats)
x="ANY"
x="CompressedRangesList"
x="NCList"
x="NCLists"
x="PartitioningByEnd"
x="PartitioningByWidth"
x="Pos"
x="Ranges"
x="RangesList"
x="Rle"
x="SimpleViewsList"

Method Definition:

function (x, ...) 
{
    width(x) - 1L + start(x)
}
<bytecode: 0x5621324a29c0>
<environment: namespace:IRanges>

Signatures:
        x        
target  "IRanges"
defined "Ranges" 
standardGeneric for "end<-" defined from package "BiocGenerics"

function (x, ..., value) 
standardGeneric("end<-")
<bytecode: 0x56212e9edb28>
<environment: 0x56212f134c40>
Methods may be defined for arguments: x
Use  showMethods("end<-")  for currently available ones.
Function: end<- (package BiocGenerics)
x="IntegerRangesList"
x="IRanges"
x="Views"

Method Definition:

function (x, ..., value) 
.set_IRanges_end(x, value)
<bytecode: 0x562132673e00>
<environment: namespace:IRanges>

Signatures:
        x        
target  "IRanges"
defined "IRanges"
standardGeneric for "width" defined from package "BiocGenerics"

function (x) 
standardGeneric("width")
<bytecode: 0x56212e6b98f0>
<environment: 0x56212e6c0108>
Methods may be defined for arguments: x
Use  showMethods("width")  for currently available ones.
Function: width (package BiocGenerics)
x="CompressedRangesList"
x="IRanges"
x="MaskCollection"
x="NCList"
x="NCLists"
x="PartitioningByEnd"
x="PartitioningByWidth"
x="Pos"
x="Ranges"
x="RangesList"
x="Rle"
x="SimpleViewsList"
x="Views"

Method Definition:

function (x) 
x@width
<bytecode: 0x56213492e638>
<environment: namespace:IRanges>

Signatures:
        x        
target  "IRanges"
defined "IRanges"
standardGeneric for "width<-" defined from package "BiocGenerics"

function (x, ..., value) 
standardGeneric("width<-")
<bytecode: 0x56212e60cd08>
<environment: 0x56212e6142b0>
Methods may be defined for arguments: x
Use  showMethods("width<-")  for currently available ones.
Function: width<- (package BiocGenerics)
x="IntegerRangesList"
x="IRanges"
x="Views"

Method Definition:

function (x, ..., value) 
.set_IRanges_width(x, value)
<bytecode: 0x562131674150>
<environment: namespace:IRanges>

Signatures:
        x        
target  "IRanges"
defined "IRanges"
standardGeneric for "pos" defined from package "BiocGenerics"

function (x) 
standardGeneric("pos")
<bytecode: 0x562130886c68>
<environment: 0x5621308869b8>
Methods may be defined for arguments: x
Use  showMethods("pos")  for currently available ones.
Function: pos (package BiocGenerics)
x="CompressedPosList"
x="IPos"
x="PosList"
x="UnstitchedIPos"

Method Definition:

function (x) 
x@pos
<bytecode: 0x5621380af758>
<environment: namespace:IRanges>

Signatures:
        x               
target  "UnstitchedIPos"
defined "UnstitchedIPos"

BiocGenerics documentation built on April 17, 2021, 6:01 p.m.