Create new scSet object

Create new scSet object

createScSet(genome, protocol = NULL, tes = NULL, genes = NULL,
  reads = NULL, n_cores = NULL, seed = 19)

Arguments

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 NULL (the default), detects the number of cores automatically. The doMC packge must be installed to register the cores.
seed

Integer. Seed for the random number generator. 19 by default.
alt_chromosomes

Logical. If FALSE (the default), restricts genome annotation to the main chromosome assembly.
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 blacklist regions are blacklisted.
whitelist

Path to bed file with whitelisted regions or GRanges object (optional). Guide off-target binding to whitelist regions are scored neutrally.
temp

Path to directory where temporary files are stored. Needs to be read- and writeable with sufficient storage space for large file sizes. If NULL (the default), is set to the return value of tempdir().
refdir

Path to search for bowtie index files. Will create new indeces in refdir if no corresponding files are found (i.e. do not match BSgenome prefix). If empty (the default), searches in the bowtie_indeces directory of the Repguide installation path.

Value

scSet object.

See also

BSgenome::available.genomes(), bowtie manual, and repeatmasker

Examples

# 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  
# }