Create new guideSet object
createGuideSet(genome, alt_chromosomes = FALSE, tes = NULL, cis = NULL, blacklist = NULL, whitelist = NULL, temp = NULL, n_cores = NULL, refdir = "", seed = 19)
genome | BSgenome object (required). Target genome assembly stored as BSgenome object. |
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alt_chromosomes | Logical. If |
tes | Path to repeatmasker output file or GRanges object with 'repname' metacolumn (required). |
cis | Path to bed file with cis regulatory feature coordinates or GRanges object (optional). |
blacklist | Path to bed file with blacklisted regions or GRanges object (optional). Guides binding to |
whitelist | Path to bed file with whitelisted regions or GRanges object (optional). Guide off-target binding to |
temp | Path to directory where temporary files are stored. Needs to be read- and writeable with sufficient storage space for large file sizes. If |
n_cores | Integer. Number of cores to use for downstream functions. If |
refdir | Path to search for bowtie index files. Will create new indeces in |
seed | Integer. Seed for the random number generator. 19 by default. |
guideSet object.