Annotation of genes affected by structural variations

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Description

Report the details of genes affected by structural variations.

Usage

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    geneAnnotation(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.. And a specific gene might be affected by multiple SVs. This function gives the detailed effects caused by structural variations to genes and its elements from the point of genes.

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

  • chr the chromosome of a structural variation.

  • start the start coordinate of a structural variation.

  • end the end coordinate of a structural variation.

Value

A data frame with the following columns:

locus

the gene affected by structural variations.

exon

the effect of structural variations to exons of a specific gene.

intron

the effect of structural variations to introns of a specific gene.

cds

the effect of structural variations to cdss of a specific gene.

utr

the effect of structural variations to utrs of a specific gene.

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)
    gene.breakdancer.anno <- llply(breakdancer,geneAnnotation,
                                   genomeAnnotation=msu_gff_v7)
    str(gene.breakdancer.anno)