svAnnotation {intansv} | R Documentation

## Annotation of structural variations

### Description

Annotate the effect caused by structural variations to genes and elements of genes.

### Usage

        svAnnotation(structuralVariation,genomeAnnotation)

### Arguments

`structuralVariation` | A data frame of structural variations.
`genomeAnnotation` | A data frame of genome annotations.

### Details

A structural variation (deletion, duplication, inversion et al.) could affect the structure of a specific gene, including deletion of introns/exons, deletion of whole gene, et al.. This function gives the detailed effects caused by structural variations to genes and elements of genes.

The parameter "structuralVariation" should be a data frame with three columns:

- chromosome the chromosome of a structural variation.

- pos1 the start coordinate of a structural variation.

- pos2 the end coordinate of a structural variation.

### Value

A data frame with the following columns:

`chromosome` | the chromosome of a structural variation.
`pos1` | the start coordinate of a structural variation.
`pos2` | the end coordinate of a structural variation.
`size` | the size of a structural variation.
`info` | information on a structural variation.
`tag` | the tag of a genomic element.
`start` | the start coordinate of a genomic element.
`end` | the end coordinate of a genomic element.
`strand` | the strand of a genomic element.
`ID` | the ID of a genomic element.

### Author(s)

Wen Yao

### Examples

        breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv",
                                       package="intansv"))
        str(breakdancer)

        msu_gff_v7 <- read.table(system.file("extdata/chr05_chr10.anno.txt", package="intansv"),
                                   head=TRUE, as.is=TRUE, sep="\t")
        breakdancer.anno <- llply(breakdancer,svAnnotation,
                                  genomeAnnotation=msu_gff_v7)
        str(breakdancer.anno)

[Package intansv version 1.24.0 Index]