Description Usage Arguments Value Examples
Given a VCF-class
object, return a vector of distances
between neighboring variants. This is useful for plotting defining
Kataegis phenomenon in a set of variants. Distance for the first
variant on each chromosome is NA.
1 |
vcf |
A |
A vector of nrow(vcf)-1 giving the distance between each variant and the previous one.
1 2 3 4 5 6 | require(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(fixed="ALT", geno=c("GT", "GL"), info=c("LDAF"))
vcf = readVcf(fl,"hg19",param=param)
d = distanceToPreviousVariant(vcf)
summary(d)
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