Description Usage Arguments Value See Also Examples
Create new scSet object
1 2 |
genome |
BSgenome object (required). Target genome assembly stored as BSgenome object. |
tes |
Path to repeatmasker output file or GRanges object with 'repname' metacolumn (required). |
n_cores |
Integer. Number of cores to use for downstream functions. If |
seed |
Integer. Seed for the random number generator. 19 by default. |
alt_chromosomes |
Logical. If |
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 |
refdir |
Path to search for bowtie index files. Will create new indeces in |
scSet object.
BSgenome::available.genomes()
, bowtie manual, and repeatmasker
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
library(BSgenome.Hsapiens.UCSC.hg38)
Path to directory containing BSgenome.Hsapiens.UCSC.hg38 bowtie indeces (e.g. BSgenome.Hsapiens.UCSC.hg38.1.ebwt, ...)
indexdir <- system.file(package = 'Repguide', 'bowtie_indeces')
# Path to TE annotation file
te_anno <- system.file(package = 'Repguide', 'extdata', 'hg38_ucsc_rmsk_ltr.txt.gz')
gs <- createscSet(genome = BSgenome.Hsapiens.UCSC.hg38, tes = te_anno, refdir = indexdir)
gs
## End(Not run)
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