Extend prime editing target to find GG sites

Extend prime editing target to find GG sites in accessible neighbourhood

extend_pe_to_gg(gr, nrt = 16, plot = FALSE)

Arguments

gr	target GRanges-class
nrt	n RT nucleotides (default 16, recommended 10-16)
plot	TRUE or FALSE (default)

Value

GRanges-class

Details

Extends each target range to the area in which to search for a prime editing GG duplet, as shown in the sketch below.

===============> ----GG---------> ----GG---------> ** <---------GG--- <---------GG---- <===============

Examples

# PE example
#-----------
    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)
    extend_pe_to_gg(gr, plot = TRUE)
#> GRanges object with 8 ranges and 3 metadata columns:
#>        seqnames              ranges strand |  targetname targetstart targetend
#>           <Rle>           <IRanges>  <Rle> | <character>   <integer> <integer>
#>   CFTR     chr7 117559584-117559598      + |        CFTR   117559593 117559595
#>   CFTR     chr7 117559590-117559604      - |        CFTR   117559593 117559595
#>    HBB    chr11     5226991-5227007      + |         HBB     5227002   5227002
#>    HBB    chr11     5226997-5227013      - |         HBB     5227002   5227002
#>   HEXA    chr15   72346572-72346585      + |        HEXA    72346580  72346583
#>   HEXA    chr15   72346578-72346591      - |        HEXA    72346580  72346583
#>   PRNP    chr20     4699589-4699605      + |        PRNP     4699600   4699600
#>   PRNP    chr20     4699595-4699611      - |        PRNP     4699600   4699600
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome