gdb.create_genome {misha} | R Documentation |
Create and Load a Genome Database
Description
This function downloads, extracts, and loads a misha genome database for the specified genome.
Usage
gdb.create_genome(genome, path = getwd(), tmpdir = tempdir())
Arguments
genome |
A character string specifying the genome to download. Supported genomes are "mm9", "mm10", "mm39", "hg19", and "hg38". |
path |
A character string specifying the directory where the genome will be extracted. Defaults to genome name (e.g. "mm10") in the current working directory. |
tmpdir |
A character string specifying the directory for storing temporary files. This is used for storing the downloaded genome file. |
Details
The function checks if the specified genome is available. If tmpdir, it constructs the download URL, downloads the genome file,
extracts it to the specified directory, and loads the genome database using gsetroot
. The function also calls gdb.reload
to reload the genome database.
Value
None.
Examples
mm10_dir <- tempdir()
gdb.create_genome("mm10", path = mm10_dir)
list.files(file.path(mm10_dir, "mm10"))
gsetroot(file.path(mm10_dir, "mm10"))
gintervals.ls()