getViewpointCoordinates: Get viewpoint coordinates

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

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
)

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.