find_primespacers {multicrispr} | R Documentation

## Find prime editing spacers

### Description

Find prime editing spacers around target ranges

### Usage

    find_primespacers(
      gr,
      bsgenome,
      edits = get_plus_seq(bsgenome, gr),
      nprimer = 13,
      nrt = 16,
      ontargetmethod = c("Doench2014", "Doench2016")[1],
      offtargetmethod = c("bowtie", "pdict")[1],
      mismatches = 0,
      nickmatches = 2,
      indexedgenomesdir = INDEXEDGENOMESDIR,
      outdir = OUTDIR,
      verbose = TRUE,
      plot = TRUE,
      ...
    )

### Arguments

`gr` | `GRanges-class`
`bsgenome` | `BSgenome-class`
`edits` | character vector: desired edits on '+' strand. If named, names should be identical to those of `gr`
`nprimer` | n primer nucleotides (default 13, max 17)
`nrt` | n rev transcr nucleotides (default 16, recomm. 10-16)
`ontargetmethod` | 'Doench2014' or 'Doench2016': on-target scoring method
`offtargetmethod` | 'bowtie' or 'pdict'
`mismatches` | no of primespacer mismatches (default 0, to suppress offtarget analysis: -1)
`nickmatches` | no of nickspacer offtarget mismatches (default 2, to suppresses offtarget analysis: -1)
`indexedgenomesdir` | directory with indexed genomes (as created by `index_genome`)
`outdir` | directory whre offtarget analysis output is written
`verbose` | TRUE (default) or FALSE
`plot` | TRUE (default) or FALSE
`...` | passed to plot_intervals

### Details

Below the architecture of a prime editing site. Edits can be performed anywhere in the revtranscript area.

spacer pam ——————–=== primer revtranscript ————-================ 1..............17....GG.......... .....................CC.......... ———-extension———-

### Value

`GRanges-class` with prime editing spacer ranges and following mcols: * crisprspacer: N20 spacers * crisprpam: NGG PAMs * crisprprimer: primer (on PAM strand) * crisprtranscript: reverse transcript (on PAM strand) * crisprextension: 3' extension of gRNA contains: reverse transcription template + primer binding site sequence can be found on non-PAM strand * crisprextrange: genomic range of crispr extension * Doench2016|4: on-target efficiency scores * off0, off1, off2: number of offtargets with 0, 1, 2 mismatches * off: total number of offtargets: off = off0 + off1 + ... * nickrange: nickspacer range * nickspacer: nickspacer sequence * nickDoench2016|4: nickspacer Doench scores * nickoff: nickspacer offtarget counts

### See Also

`find_spacers` to find standard crispr sites

### Examples

    # Find PE spacers for 4 clinically relevant loci (Anzalone et al, 2019)
        bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
        gr <- char_to_granges(c(
            PRNP = 'chr20:4699600:+',             # snp: prion disease
            HBB  = 'chr11:5227002:-',             # snp: sickle cell anemia
            HEXA = 'chr15:72346580-72346583:-',   # del: tay sachs disease
            CFTR = 'chr7:117559593-117559595:+'), # ins: cystic fibrosis
            bsgenome)
        spacers <- find_primespacers(gr, bsgenome)
        spacers <- find_spacers(extend_for_pe(gr), bsgenome, complement = FALSE)

    # Edit PRNP locus for resistance against prion disease (Anzalone et al, 2019)
        bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
        gr <- char_to_granges(c(PRNP = 'chr20:4699600:+'), bsgenome)
        find_primespacers(gr, bsgenome)
        find_primespacers(gr, bsgenome, edits = 'T')

[Package multicrispr version 1.4.3 Index]