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.