rtDetect {StructuralVariantAnnotation} | R Documentation |
Detecting retrotranscript insertion in nuclear genomes.
rtDetect(gr, genes, maxgap = 100, minscore = 0.3)
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.