score_ontargets {multicrispr} | R Documentation |
Add Doench2014 or Doench2016 on-target efficiency scores
score_ontargets( spacers, bsgenome, ontargetmethod = c("Doench2014", "Doench2016")[1], chunksize = 10000, verbose = TRUE, plot = TRUE, ... )
spacers |
|
bsgenome |
|
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 |
add_ontargets
adds efficiency scores
filter_ontargets
adds efficiency scores and filters on them
numeric vector
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
# 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')