rtDetect {svaRetro} | R Documentation

## Detecting retrotranscript insertion in nuclear genomes.

### Description

Detecting retrotranscript insertion in nuclear genomes.

### Usage

    rtDetect(gr, genes, maxgap = 100, minscore = 0.4)

### Arguments

`gr` | A GRanges object
`genes` | TxDb object of genes. hg19 and hg38 are supported in the current version.
`maxgap` | The maxium distance allowed on the reference genome between the paired exon boundries.
`minscore` | The minimum proportion of intronic deletions of a transcript should be identified.

### Details

This function searches for retroposed transcripts by identifying breakpoints supporting intronic deletions and fusions between exons and remote loci. Only BND notations are supported at the current stage.

### Value

A GRangesList object, named insSite and rt, reporting breakpoints supporting insert sites and retroposed transcripts respectively. 'exon' and 'txs' in the metadata columns report exon_id and transcript_name from the 'genes' object.

### Examples

    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    genes <- TxDb.Hsapiens.UCSC.hg19.knownGene
    vcf.file <- system.file("extdata", "diploidSV.vcf",
                             package = "svaRetro")
    vcf <- VariantAnnotation::readVcf(vcf.file, "hg19")
    gr <- breakpointRanges(vcf, nominalPosition=TRUE)
    rt <- rtDetect(gr, genes, maxgap=30, minscore=0.6)

[Package svaRetro version 1.0.0 Index]