StructuralVariant-class: The StructuralVariant class stores data pertaining to somatic...
In cancer-genomics/trellis: Somatic structural variant analysis

readPairs

R Documentation

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.