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 1.4.3 Index]