Breakpoints-class {R453Plus1Toolbox} | R Documentation

## Class "Breakpoints"

### Description

Container to store chimeric reads that were clustered to putative breakpoints indicating structural variants. Related information like breakpoint position or alignment information about the chimeric reads is stored as well.

### Objects from the Class

Objects can be created by calls of the form `new("Breakpoints", ...)`. Usually, objects will be created by calling the `detectBreakpoints` method. It is not intended that users create objects of this class manually.

All slots of this class can be found twice. One slot name ends with “C1” and the other “C2”. The slots labeled with “C2” are empty until `mergeBreakpoints` has been called and contain information about putativly associated breakpoints detected by `mergeBreakpoints`.

### Slots

`seqsC1`:

  Object of class `"list"` with one data frame for each breakpoint. The data frame stores all chimeric reads covering the first breakpoint together with the alignment information.

`seqsC2`:

  Object of class `"list"` with one data frame for each breakpoint. The data frame stores all chimeric reads covering the second breakpoint together with the alignment information.

`commonBpsC1`:

  Object of class `"list"` with one data frame for each breakpoint. The data frame stores the consensus breakpoint sequence as well as the breakpoint coordinates of the first breakpoint.

`commonBpsC2`:

  Object of class `"list"` with one data frame for each breakpoint. The data frame stores the consensus breakpoint sequence as well as the breakpoint coordinates of the second breakpoint.

`commonAlignC1`:

  Object of class `"list"` with one object of class `PairwiseAlignmentsSingleSubject-class` for each breakpoint storing the alignments of the chimeric reads against the consensus breakpoint sequence for the first breakpoint.

`commonAlignC2`:

  Object of class `"list"` with one object of class `PairwiseAlignmentsSingleSubject-class` for each breakpoint storing the alignments of the chimeric reads against the consensus breakpoint sequence for the second breakpoint.

`alignedReadsC1`:

  Object of class `"list"` with one object of class `AlignedRead-class` storing all chimeric reads covering the first breakpoint and their alignments.

`alignedReadsC2`:

  Object of class `"list"` with one object of class `AlignedRead-class` storing all chimeric reads covering the second breakpoint and their alignments.

### Methods

alignedReadsC1<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the alignedReadsC1 slot.

alignedReadsC1

  `signature(object = "Breakpoints")`: Getter-method for the alignedReadsC1 slot.

alignedReadsC2<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the alignedReadsC2 slot.

alignedReadsC2

  `signature(object = "Breakpoints")`: Getter-method for the alignedReadsC2 slot.

commonAlignC1<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the commonAlignC1 slot.

commonAlignC1

  `signature(object = "Breakpoints")`: Getter-method for the commonAlignC1 slot.

commonAlignC2<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the commonAlignC2 slot.

commonAlignC2

  `signature(object = "Breakpoints")`: Getter-method for the commonAlignC2 slot.

commonBpsC1<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the commonBpsC1 slot.

commonBpsC1

  `signature(object = "Breakpoints")`: Getter-method for the commonBpsC1 slot.

commonBpsC2<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the commonBpsC2 slot.

commonBpsC2

  `signature(object = "Breakpoints")`: Getter-method for the commonBpsC2 slot.

seqsC1<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the seqsC1 slot.

seqsC1

  `signature(object = "Breakpoints")`: Getter-method for the seqsC1 slot.

sqsC2<-

  `signature(object = "Breakpoints", value = "list")`: Setter-method for the seqsC2 slot.

seqsC2

  `signature(object = "Breakpoints")`: Getter-method for the seqsC2 slot.

[

  `signature(x = "Breakpoints", i = "ANY", j = "ANY")`: Subsetting a Breakpoints object.

length

  `signature(x = "Breakpoints")`: Returns the number of breakpoints stored.

mergeBreakpoints

  `signature(breakpoints = "Breakpoints", maxDist = "missing", mergeBPs = "list")`: Merge presumably related breakpoints.

mergeBreakpoints

  `signature(breakpoints = "Breakpoints", maxDist = "missing", mergeBPs = "missing")`: Merge presumably related breakpoints.

mergeBreakpoints

  `signature(breakpoints = "Breakpoints", maxDist = "numeric", mergeBPs = "missing")`: Merge presumably related breakpoints.

names<-

  `signature(x = "Breakpoints", value = "ANY")`: Set the names of the breakpoints.

names

  `signature(x = "Breakpoints")`: Get the names of the breakpoints.

plotChimericReads

  `signature(brpData = "Breakpoints")`: Plot the structural variant and the chimeric reads covering its breakpoints.

summary

  `signature(object = "Breakpoints")`: Create a data frame summaring information about all breakpoints.

table

  `signature(... = "Breakpoints")`: Create a frequency table of cluster sizes.

### Author(s)

Hans-Ulrich Klein, Christoph Bartenhagen

### See Also

`filterChimericReads`, `detectBreakpoints`, `mergeBreakpoints`, `plotChimericReads`

[Package R453Plus1Toolbox version 1.30.0 Index]