index_genome {multicrispr}R Documentation

Index genome

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())

[Package multicrispr version 1.4.3 Index]