svAnnotation: Annotation of structural variations

Description Usage Arguments Details Value Author(s) Examples

View source: R/svAnnotation.R

Description

Annotate the effect caused by structural variations to genes and elements of genes.

Usage

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    svAnnotation(structuralVariation,genomeAnnotation)

Arguments

structuralVariation

A data frame of structural variations.

genomeAnnotation

A data frame of genome annotations.

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.. This function gives the detailed effects caused by structural variations to genes and elements of genes.

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

Value

A data frame with the following columns:

chromosome

the chromosome of a structural variation.

pos1

the start coordinate of a structural variation.

pos2

the end coordinate of a structural variation.

size

the size of a structural variation.

info

information on a structural variation.

tag

the tag of a genomic element.

start

the start coordinate of a genomic element.

end

the end coordinate of a genomic element.

strand

the strand of a genomic element.

ID

the ID of a genomic element.

Author(s)

Wen Yao

Examples

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    breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv",
                                   package="intansv"))
    str(breakdancer)

    msu_gff_v7 <- read.table(system.file("extdata/chr05_chr10.anno.txt", package="intansv"),
                               head=TRUE, as.is=TRUE, sep="\t")
    breakdancer.anno <- llply(breakdancer,svAnnotation,
                              genomeAnnotation=msu_gff_v7)
    str(breakdancer.anno)

intansv documentation built on July 21, 2018, 6 p.m.