extend_for_pe {multicrispr}R Documentation

Extend ranges for prime editing

Description

Extend target ranges to span in which to look for spacer-pam seqs

Usage

extend_for_pe(
  gr,
  bsgenome,
  nrt = 16,
  spacer = strrep("N", 20),
  pam = "NGG",
  plot = FALSE
)

Arguments

gr

GRanges-class

bsgenome

BSgenome-class

nrt

number: reverse transcription length

spacer

string: spacer pattern in extended IUPAC alphabet

pam

string: pam pattern in extended IUPAC alphabet

plot

TRUE (default) or FALSE

Details

Extend target ranges to find nearby spacers for prime editing

Value

GRanges-class

Examples

require(magrittr)
bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38  
gr <- char_to_granges(c( PRNP = 'chr20:4699600:+',             # snp
                         HBB  = 'chr11:5227002:-',             # snp
                         HEXA = 'chr15:72346580-72346583:-',   # del
                         CFTR = 'chr7:117559593-117559595:+'), # ins
                     bsgenome = bsgenome)
find_primespacers(gr, bsgenome)
(grext <- extend_for_pe(gr))
find_spacers(grext, bsgenome, complement = FALSE)

[Package multicrispr version 1.3.0 Index]