Annotation of structural variations

Description

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

Usage

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    svAnnotation(structuralVariation,genomeAnnotation)

Arguments

structuralVariation

A data frame of structural variations.

genomeAnnotation

A genomic ranges of the genome annotation.

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:

chr

the chromosome of a structural variation.

start

the start coordinate of a structural variation.

end

the end coordinate of a structural variation.

overlap

the overlap length between a structural variation and a specific gene or its element.

annotation

the annotation of a specific gene that overlap with the structural variation.

parent

the ID of a specific gene that overlap with the structural variation.

Author(s)

Wen Yao

Examples

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

    load(system.file("extdata/genome.anno.RData",package="intansv"))
    str(msu_gff_v7)
    breakdancer.anno <- llply(breakdancer,svAnnotation,
                              genomeAnnotation=msu_gff_v7)
    str(breakdancer.anno)