numtDetect {svaNUMT} | R Documentation |
Detecting nuclear mitochondria fusion events.
numtDetect(gr, max_ins_dist = 10)
gr |
A GRanges object |
max_ins_dist |
The maximum distance allowed on the reference genome between the paired insertion sites. Only intra-chromosomal NUMT events are supported. Default value is 10. |
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 by chromosome in GRanges format.
A nested list of GRanges objects of candidate NUMTs.
vcf.file <- system.file("extdata", "MT.vcf", package = "svaNUMT") vcf <- VariantAnnotation::readVcf(vcf.file, "hg19") gr <- breakpointRanges(vcf, nominalPosition=TRUE) numt.gr <- numtDetect(gr, max_ins_dist=20)