RearrangementList-class: Constructor for 'RearrangementList' class

In cancer-genomics/trellis: Somatic structural variant analysis

Constructor for RearrangementList class

Description

A given sample may have multiple rearrangements. It is convenient to encapsulate the data supporting each rearrangement in a Rearrangement object, and to list all of these rearrangements in a RearrangementList.

Usage

RearrangementList(object, modal_rearrangement, percent_rearrangement, colData)

## S4 method for signature 'missing'
RearrangementList(object, colData)

## S4 method for signature 'list'
RearrangementList(object, colData)

## S4 method for signature 'Rearrangement'
RearrangementList(object)

## S4 method for signature 'RearrangementList'
colData(x, ...)

## S4 replacement method for signature 'RearrangementList,ANY'
colData(x) <- value

## S4 method for signature 'RearrangementList'
elementType(x, ...)

## S4 method for signature 'RearrangementList'
length(x)

## S4 method for signature 'RearrangementList'
names(x)

## S4 method for signature 'RearrangementList,GRanges'
overlapsAny(
  query,
  subject,
  maxgap = -1L,
  minoverlap = 0L,
  type = c("any", "start", "end", "within", "equal"),
  ...
)

## S4 replacement method for signature 'RearrangementList'
x$name <- value

## S4 method for signature 'RearrangementList'
x$name

## S4 method for signature 'RearrangementList,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'RearrangementList,ANY,ANY'
x[[i, j, ..., drop = FALSE]]

## S4 replacement method for signature 'RearrangementList,ANY,ANY,ANY'
x[[i, j, ..., drop = FALSE]] <- value

## S4 method for signature 'RearrangementList'
c(x, ..., recursive = FALSE)

## S4 method for signature 'RearrangementList'
seqlevels(x)

Arguments

object	a list of Rearrangement objects
modal_rearrangement	a character vector of the modal rearrangement corresponding to each element in object. Must be the same length as object.
percent_rearrangement	a numeric vector indicating the fraction of improper read pairs supporting the modal rearrangement type. Must be the same length as object.
colData	a DataFrame containing metadata on the Rearrangement objects.
x	a RearrangementList object
...	ignored
query	a RearrangementList
subject	a GRanges object
i	a numeric or character vector of rearrangement names
j	ignored
drop	ignored

Value

a RearrangementList object

RearrangementList

a Rearrangement object

a Rearrangement object

Slots

data

a list of Rearrangement objects

elementType

a character vector

names

a charcter vector of names. Must have the same length as the list object.

colData

a DataFrame

modal_rearrangement

a character vector

percent_rearrangement

a numeric vector

See Also

Rearrangement

Rearrangement

Examples

RearrangementList()

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.