Description Usage Arguments Details Value Author(s) Examples
Functions for identifying variant types such as SNVs, insertions, deletions, transitions, and structural rearrangements.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | ## 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)
|
x |
A VCF or VRanges object. |
singleAltOnly |
A When |
... |
Arguments passed to other methods. |
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).
A logical
vector the same length as x
.
Michael Lawrence, Valerie Obenchain and Robert Castelo
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | 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)
|
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