| Title: | Retrotransposed transcript detection from structural variants |
|---|---|
| Description: | svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts. |
| Authors: | Ruining Dong [aut, cre] |
| Maintainer: | Ruining Dong <[email protected]> |
| License: | GPL-3 + file LICENSE |
| Version: | 1.11.0 |
| Built: | 2024-07-01 05:50:15 UTC |
| Source: | https://github.com/bioc/svaRetro |
Replaces the NA values in a with corresponding values in b
a %na% ba %na% b
a, b
|
objects to be tested or coerced. |
The altered object.
Uses b if a is NULL
a %null% ba %null% b
a, b
|
objects to be tested or coerced. |
An un-null object.
Detecting retrotranscript insertion in nuclear genomes.
rtDetect(gr, genes, maxgap = 100, minscore = 0.4)rtDetect(gr, genes, maxgap = 100, minscore = 0.4)
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. |
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.
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.
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)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)
svaRetro contains functions for detecting retrotransposed transcripts from structural variant calls.
For more details on the features of StructuralVariantAnnotation, read the vignette: 'browseVignettes(package = "svaRetro")'