svAnnotation: Annotation of structural variations

In intansv: Integrative analysis of structural variations

Description

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

Usage

    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:

• chromosome the chromosome of a structural variation.

• pos1 the start coordinate of a structural variation.

• pos2 the end coordinate of a structural variation.

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

    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 Nov. 8, 2020, 5:15 p.m.