plotRegion: Display structural variations in a specific genomic region

In venyao/intansv: Integrative analysis of structural variations

Display structural variations in a specific genomic region

Description

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

Usage

    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:

• 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

    delly <- readDelly(system.file("extdata/ZS97.DELLY.vcf",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)

venyao/intansv documentation built on Jan. 3, 2024, 6:15 p.m.