extend_for_pe {multicrispr} | R Documentation |
Extend target ranges to span in which to look for spacer-pam seqs
extend_for_pe( gr, bsgenome, nrt = 16, spacer = strrep("N", 20), pam = "NGG", plot = FALSE )
gr |
|
bsgenome |
|
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 |
Extend target ranges to find nearby spacers for prime editing
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)