plotChromosome: Display the chromosome distribution of structural variations

Description Usage Arguments Details Value Author(s) Examples

View source: R/plotChromosome.R

Description

Display the chromosome distribution of structural variations by splitting the chromosomes into windows of specific size and counting the number of structural variations in each window.

Usage

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    plotChromosome(genome, structuralVariation, windowSize=1000000)

Arguments

genome

A data frame with ID and length of all Chromosomes.

structuralVariation

A list of structural variations.

windowSize

A specific size (in base pair) to split chromosomes into windows.

Details

To visualize the distribution of structural variations in the whole genome, chromosomes were splitted into windows of specific size (default 1 Mb) and the number of structural variations in each window were counted. The number of structural variations were shown using circular barplot.

Value

A circular plot with five layers:

Author(s)

Wen Yao

Examples

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

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

    plotChromosome(genome,delly,1000000)
	

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