distanceToPreviousVariant: Find the distance between each variant and the previous one
In seandavi/MutationTools: What the package does (short line)
Description
Usage
Arguments
Value
Examples
Description
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.
Usage
1
Arguments
vcf
A VCF-class
Value
A vector of nrow(vcf)-1 giving the distance between
each variant and the previous one.
Examples
1
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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)
seandavi/MutationTools documentation built on May 29, 2019, 4:32 p.m.
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Description Usage Arguments Value Examples
Description
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.
Usage
1 |
Arguments
vcf |
A |
Value
A vector of nrow(vcf)-1 giving the distance between each variant and the previous one.
Examples
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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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