bsj_to_circRNA_sequence: bsj_to_circRNA_sequence

In Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Description

Takes one BSJ coordinate and generates a predicted circular RNA sequence.

Usage

bsj_to_circRNA_sequence(BSJ, geneID = NULL, genome, TxDb,
  annotationLibrary)

Arguments

BSJ	: BSJ coordinate in the format of chr_coordinate_chr_coorindate OR chr:coordinate-coorindate:strand.
geneID	: The gene ID that the BSJ aligns to. Not essential as this can be identified from the BSJ coordinate, however time performance of function improved if this information can be provided.
genome	: Is the length f the library fragment
TxDb	: The sequence read length
annotationLibrary	: annotation database. See details for example.

Value

Returns a DNAstring object.

Examples

library('Ularcirc')
library('BSgenome.Hsapiens.UCSC.hg38')
library('TxDb.Hsapiens.UCSC.hg38.knownGene')
TxDb <- TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
annotationLibrary <- org.Hs.eg.db::org.Hs.eg.db

# Define BSJ. Following two formats are accepted
BSJ <- 'chr2:40430305-40428472:-'       # SLC8A1
BSJ  <- 'chr2_40430305_chr2_40428472'   # SLC8A1

circRNA_sequence <- bsj_to_circRNA_sequence(BSJ, "SLC8A1", genome,TxDb, annotationLibrary)

# You can also retrieve sequence without passing gene annotation - but this is slower
# circRNA_sequence <- bsj_to_circRNA_sequence(BSJ, NULL, genome,TxDb, annotationLibrary)

Ularcirc documentation built on Nov. 8, 2020, 6:34 p.m.