Display structural variations in a specific genomic region

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Description

Display the structural variations in a specific genomic region in circular view.

Usage

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    plotRegion(structuralVariation, genomeAnnotation, 
               regionChromosome, regionStart, regionEnd)

Arguments

structuralVariation

A list of structural variations.

genomeAnnotation

A genomic ranges of the genome annotation.

regionChromosome

The chromosome identifier of a specific region to view.

regionStart

The start coordinate of a specific region to view.

regionEnd

The end coordinate of a specific region to view.

Details

Different SVs were shown as rectangles in different layers. See the package vignette and the example dataset for more details.

Value

A circular plot of all the structural variations and genes in a specific region with four layers:

  • The composition of genes of a specific genomic region.

  • The composition of deletions of a specific genomic region.

  • The composition of duplications of a specific genomic region.

  • The composition of inversions of a specific genomic region.

Author(s)

Wen Yao

Examples

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    delly <- readDelly(system.file("extdata/delly",package="intansv"))
    str(delly)

    load(system.file("extdata/genome.anno.RData",package="intansv"))
    str(msu_gff_v7)

    plotRegion(delly,msu_gff_v7,"chr05",1,200000)