StructuralVariant-class: The StructuralVariant class stores data pertaining to somatic...

In cancer-genomics/trellis: Somatic structural variant analysis

The StructuralVariant class stores data pertaining to somatic deletions

Description

StructuralVariant is a vector-like class for storing genomic intervals of somatic deletions and relevant supporting data. Properly and improperly paired reads and indices so that subsetting methods ([) extracts the relevant data for a given deletion.

Usage

readPairs(object)

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

StructuralVariant(
  variant = GRanges(),
  proper = .GAlignmentPairs(),
  improper = .GAlignmentPairs(),
  copynumber,
  calls,
  index_proper,
  index_improper,
  grouped_variant
)

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

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

## S4 method for signature 'StructuralVariant'
readPairs(object)

## S4 method for signature 'StructuralVariant'
sort(x, decreasing = FALSE, ...)

## S4 method for signature 'StructuralVariant'
variant(object)

## S4 replacement method for signature 'StructuralVariant,ANY'
variant(object) <- value

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

## S4 method for signature 'StructuralVariant,ANY,ANY'
x[[i]]

## S4 replacement method for signature 'StructuralVariant,GRanges'
variant(object) <- value

## S4 method for signature 'StructuralVariant'
improper(object)

## S4 method for signature 'StructuralVariant'
seqlengths(x)

## S4 method for signature 'StructuralVariant'
seqinfo(x)

Arguments

object	a StructuralVariant
x	a StructuralVariant
...	ignored
variant	a GRanges object of the deletion genomic intervals
proper	a GAlignmentPairs object of proper read pairs near the deletion
improper	a GAlignmentPairs object of improper read pairs near the deletion
copynumber	the mean log2 ratio (derived from read depth) of the deletion region
calls	character vector indicating the type of deletion (hemizygous, hemizygous+, homozygous , homozygous+, overlapping hemizygous)
index_proper	integer vector used internally for subsetting
index_improper	integer vector used internally for subsetting
grouped_variant	a grouping factor for the deletion intervals
decreasing	logical

Slots

variant

A GRanges object

proper

A GAlignmentPairs object of properly paired reads

improper

A GAlignmentPairs object of improperly paired reads

copynumber

A numeric vector of the mean log ratios corresponding to the variant intervals. The numeric vector must have the same length as variant.

calls

A length-N character vector of deletion calls where N is the number of intervals in variant. Possible calls are (i) hemizygous: hemizygous deletion with fewer than 5 supporting improper read pairs (ii) hemizygous+: hemizygous deletion with 5 or more supporting improper read pairs (iii) homozygous: homozygous deletion with fewer than 5 supporting improper read pairs (iv) homozygous+: homozygous deletion with 5 or more supporting improper read pairs

index_proper

a list of indices. Each element is a vector of integers. The kth element are the elements of the GAlignmentPairs object in slot proper supporting the kth deletion.

index_improper

A list of indices. Each element is a vector of integers. The kth element are the elements of the GAlignmentPairs object in slot improper supporting the kth deletion.

grouped_variant

a factor indicating whether deletions belong to the same group (e.g., overlapping hemizygous deletions)

length_improper

Keeps track of the numer of the total number of improper read pairs for quick summaries of this object.

length_proper

Keeps track of the numer of the total number of proper read pairs for quick summaries of this object.

Examples

StructuralVariant()

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