numtDetect: Detecting nuclear mitochondria fusion events.

In PapenfussLab/StructuralVariantAnnotation: Variant annotations for structural variants

Description

Detecting nuclear mitochondria fusion events.

Usage

numtDetect(gr, nonStandardChromosomes = FALSE, max_ins_dist = 1000)

Arguments

gr	A GRanges object
nonStandardChromosomes	Whether to report insertion sites on non-standard reference chromosomes. Default value is set to FALSE.
max_ins_dist	The maxium distance allowed on the reference genome between the paired insertion sites. Only intra-chromosomal NUMT events are supported. Default value is 1000.

Details

Nuclear mitochondrial fusion (NUMT) is a common event found in human genomes. This function searches for NUMT events by identifying breakpoints supporting the fusion of nuclear chromosome and mitochondrial genome. Only BND notations are supported at the current stage. Possible linked nuclear insertion sites are reported using SV IDs in the candidatePartnerId metadata column.

Value

A GRanges object of possible NUMT loci.

Examples

vcf.file <- system.file("extdata", "MT.vcf", package = "StructuralVariantAnnotation")
vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
gr <- breakpointRanges(vcf, nominalPosition=TRUE)
numt.gr <- numtDetect(gr)

PapenfussLab/StructuralVariantAnnotation documentation built on Dec. 25, 2021, 1:20 a.m.