extend_for_pe: Extend ranges for prime editing

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

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)

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.