add_genome_matches {multicrispr} | R Documentation

## Add genome matches

### Description

Add genome matches

### Usage

    add_genome_matches(
      spacers,
      bsgenome = getBSgenome(genome(spacers)[1]),
      mismatches = 2,
      pam = "NGG",
      offtargetmethod = c("bowtie", "pdict")[1],
      outdir = OUTDIR,
      indexedgenomesdir = INDEXEDGENOMESDIR,
      verbose = TRUE
    )

### Arguments

`spacers` | GRanges
`bsgenome` | BSgenome
`mismatches` | number
`pam` | string
`offtargetmethod` | 'bowtie' or 'pdict'
`outdir` | bowtie output directory
`indexedgenomesdir` | directory with indexed genomes
`verbose` | TRUE (default) or FALSE

### Value

GRanges

### Examples

    require(magrittr)
    file <- system.file('extdata/SRF.bed', package='multicrispr')
    bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
    targets0 <- bed_to_granges(file, 'mm10')
    targets <- extend(targets0)
    spacers <- find_spacers(targets, bsgenome, complement = FALSE,
                            ontargetmethod = NULL, offtargetmethod = NULL)
    spacers %<>% extract(1:100)
    spacers %<>% add_genome_matches(bsgenome)

[Package multicrispr version 1.4.3 Index]