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

Description Usage Arguments Value See Also Examples

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

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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

Examples

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## 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:BiocGenericsThe following objects are masked frompackage:parallel:

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

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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:S4VectorsThe following object is masked frompackage: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.