plotRegion: Display structural variations in a specific genomic region

Description Usage Arguments Details Value Author(s) Examples

View source: R/plotRegion.R

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 data frame of genome annotations.

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:

Author(s)

Wen Yao

Examples

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

    anno.file.path <- system.file("extdata/chr05_chr10.anno.txt", package="intansv")
    msu_gff_v7 <- read.table(anno.file.path, head=TRUE, as.is=TRUE)
    str(msu_gff_v7)

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

intansv documentation built on Nov. 17, 2017, 1:32 p.m.