isSNV {VariantAnnotation} | R Documentation |
Functions for identifying variant types such as SNVs, insertions, deletions, transitions, and structural rearrangements.
## 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 |
|
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
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)