isSNV {VariantAnnotation} | R Documentation

## Identification of genomic variant types.

### Description

Functions for identifying variant types such as SNVs, insertions, deletions, transitions, and structural rearrangements.

### Usage

    ## S4 method for signature 'VRanges'
    isSNV(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isSNV(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isSNV(x, ..., singleAltOnly = TRUE)

    ## S4 method for signature 'VRanges'
    isInsertion(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isInsertion(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isInsertion(x, ..., singleAltOnly = TRUE)

    ## S4 method for signature 'VRanges'
    isDeletion(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isDeletion(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isDeletion(x, ..., singleAltOnly = TRUE)

    ## S4 method for signature 'VRanges'
    isIndel(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isIndel(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isIndel(x, ..., singleAltOnly = TRUE)

    ## S4 method for signature 'VRanges'
    isDelins(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isDelins(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isDelins(x, ..., singleAltOnly = TRUE)

    ## S4 method for signature 'VRanges'
    isTransition(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isTransition(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isTransition(x, ..., singleAltOnly = TRUE)

    ## S4 method for signature 'VRanges'
    isSubstitution(x, ...)
    ## S4 method for signature 'ExpandedVCF'
    isSubstitution(x, ...)
    ## S4 method for signature 'CollapsedVCF'
    isSubstitution(x, ..., singleAltOnly = TRUE)

### Arguments

`x` | A VCF or VRanges object.
`singleAltOnly` | A `logical` only applicable when `x` is a CollapsedVCF class. When `TRUE` (default) only variants with a single alternate allele are evaluated; all multi-alt variants evaluate to `FALSE`. When `singleAltOnly=FALSE` all ref / alt pairs for each variant are evaluated. If any ref / alt pairs meet the test criteria a value of TRUE is returned for the variant; this may result in a value of TRUE for a variant with a mixture of alternate alleles, some that pass the criteria and some that do not. To retain single ref / alt pairs that pass the critera use `expand` on the `CollapsedVCF` and then apply the test.
`...` | Arguments passed to other methods.

### Details

All functions return a logical vector the length of `x`. Variants in gvcf files with NON_REF alt alleles return TRUE; structural variants return FALSE.

- isSNV: Reference and alternate alleles are both a single nucleotide long.

- isInsertion: Reference allele is a single nucleotide and the alternate allele is greater (longer) than a single nucleotide and the first nucleotide of the alternate allele matches the reference.

- isDeletion: Alternate allele is a single nucleotide and the reference allele is greater (longer) than a single nucleotide and the first nucleotide of the reference allele matches the alternate.

- isIndel: The variant is either a deletion or insertion as determined by `isDeletion` and `isInsertion`.

- isDelins: The variant is a deletion followed by an insertion, either of them involving two or more nucleotides.

- isSubstition: Reference and alternate alleles are the same length (1 or more nucleotides long).

- isTransition: Reference and alternate alleles are both a single nucleotide long. The reference-alternate pair interchange is of either two-ring purines (A <-> G) or one-ring pyrimidines (C <-> T).

### Value

A `logical` vector the same length as `x`.

### Author(s)

Michael Lawrence, Valerie Obenchain and Robert Castelo

### Examples

      fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
      ## ---------------------------------------------------------------------
      ## VCF objects
      ## ---------------------------------------------------------------------
      vcf <- readVcf(fl, "hg19")
      DataFrame(ref(vcf), alt(vcf))

      ## This vcf has transitions in row 2 and 3. When 'singleAltOnly=TRUE'
      ## only the row 2 variant is identified:
      isTransition(vcf)

      ## Both row 2 and 3 are identified when 'singleAltOnly=FALSE':
      isTransition(vcf, singleAltOnly=FALSE)

      ## Expand the CollapsedVCF to ExpandedVCF
      evcf <- expand(vcf)

      ## All ref / alt pairs are now expanded and there is no need to
      ## use 'singleAltOnly'. The return length is now 7 instead of 5:
      transition <- isTransition(evcf)
      transition
      DataFrame(ref(evcf)[transition], alt(evcf)[transition])

      ## ---------------------------------------------------------------------
      ## VRanges objects
      ## ---------------------------------------------------------------------
      ## A VRanges object holds data from a VCF class in a completely
      ## 'flat' fashion. INFO and FORMAT variables for all subjects are
      ## 'repped' out such that each row is a unique combination of data.
      vr <- as(vcf, "VRanges")
      isSNV(vr, singleAltOnly=FALSE)

[Package VariantAnnotation version 1.24.5 Index]