score_ontargets {multicrispr} | R Documentation

## Add on-target efficiency scores

### Description

Add Doench2014 or Doench2016 on-target efficiency scores

### Usage

    score_ontargets(
      spacers,
      bsgenome,
      ontargetmethod = c("Doench2014", "Doench2016")[1],
      chunksize = 10000,
      verbose = TRUE,
      plot = TRUE,
      ...
    )

### Arguments

`spacers` | `GRanges-class`: spacers
`bsgenome` | `BSgenome-class`
`ontargetmethod` | 'Doench2014' (default) or 'Doench2016' (requires non-NULL argument python, virtualenv, or condaenv)
`chunksize` | Doench2016 is executed in chunks of chunksize
`verbose` | TRUE (default) or FALSE
`plot` | TRUE (default) or FALSE
`...` | passed to `plot_intervals`

### Details

`add_ontargets` adds efficiency scores `filter_ontargets` adds efficiency scores and filters on them

### Value

numeric vector

### References

Doench 2014, Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nature Biotechnology, doi: 10.1038/nbt.3026

Doench 2016, Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nature Biotechnology, doi: 10.1038/nbt.3437

Python module azimuth: github/MicrosoftResearch/azimuth

### Examples

    # Install azimuth
    #----------------
        ## With reticulate
        # require(reticulate)
        # conda_create('azienv', c('python=2.7'))
        # use_condaenv('azienv')
        # py_install(c('azimuth', 'scikit-learn==0.17.1', 'biopython=='1.76'),
        #            'azienv', pip = TRUE)

        ## Directly
        # conda create --name azienv python=2.7
        # conda activate azienv
        # pip install scikit-learn==0.17.1
        # pip install biopython==1.76
        # pip install azimuth

    # PE example
    #-----------
        require(magrittr)
        bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
        targets <- char_to_granges(c(PRNP = 'chr20:4699600:+',             # snp
                                     HBB  = 'chr11:5227002:-',             # snp
                                     HEXA = 'chr15:72346580-72346583:-',   # del
                                     CFTR = 'chr7:117559593-117559595:+'), # ins
                                   bsgenome)
        spacers <- find_primespacers(targets, bsgenome, ontargetmethod=NULL,
                                    offtargetmethod=NULL)
        spacers %<>% score_ontargets(bsgenome, 'Doench2014')
        # reticulate::use_condaenv('azienv')
        # reticulate::import('azimuth')
        # spacers %<>% score_ontargets(bsgenome, 'Doench2016')

    # TFBS example
    #-------------
        bedfile  <- system.file('extdata/SRF.bed', package = 'multicrispr')
        bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
        targets <- extend(bed_to_granges(bedfile, 'mm10'))
        spacers <- find_spacers(targets, bsgenome, ontargetmethod=NULL,
                                offtargetmethod=NULL)
        spacers %<>% score_ontargets(bsgenome, 'Doench2014')
        # reticulate::use_condaenv('azienv')
        # reticulate::import('azimuth')
        # spacers %>%  score_ontargets(bsgenome, 'Doench2016')

[Package multicrispr version 1.4.3 Index]