index_genome: Index genome

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

Description

Bowtie index genome

Usage

index_genome(
  bsgenome,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  download = TRUE,
  overwrite = FALSE
)

Arguments

bsgenome	BSgenome-class
indexedgenomesdir	string: directory with bowtie-indexed genome
download	TRUE (default) or FALSE: whether to download pre-indexed version if available
overwrite	TRUE or FALSE (default)

Details

Checks whether already available locally. If not, checks whether indexed version can be downloaded from our s3 storage. If not, builds the index with bowtie. This can take a few hours, but is a one-time operation.

Value

invisible(genomdir)

Examples

bsgenome <- BSgenome.Scerevisiae.UCSC.sacCer1::Scerevisiae
index_genome(bsgenome, indexedgenomesdir = tempdir())

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.