getViewpointCoordinates {UMI4Cats} | R Documentation

## Get viewpoint coordinates

### Description

Finds the viewpoint coordinates for a given reference genome and sequence.

### Usage

    getViewpointCoordinates(
      bait_seq,
      bait_pad,
      res_enz,
      ref_gen,
      sel_seqname = NULL
    )

### Arguments

`bait_seq` | Character containing the bait primer sequence.
`bait_pad` | Character containing the pad sequence (sequence between the bait primer and the restriction enzyme sequence).
`res_enz` | Character containing the restriction enzyme sequence.
`ref_gen` | A BSgenome object of the reference genome.
`sel_seqname` | A character with the chromosome name to focus the search for the viewpoint sequence.

### Value

Creates a GRanges object containing the genomic position of the viewpoint.

### Examples

    getViewpointCoordinates(
        bait_seq = "GGACAAGCTCCCTGCAACTCA",
        bait_pad = "GGACTTGCA",
        res_enz = "GATC",
        ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
        sel_seqname = "chr16" # Look only in chr16
    )

[Package UMI4Cats version 1.2.1 Index]