bsj_to_circRNA_sequence {Ularcirc} | R Documentation

## bsj_to_circRNA_sequence

### 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)

[Package Ularcirc version 1.4.0 Index]