gdb.create: Creates a new Genomic Database
In misha: Toolkit for Analysis of Genomic Data

gdb.create

R Documentation

Creates a new Genomic Database

Description

Creates a new Genomic Database.

Usage

gdb.create(
  groot = NULL,
  fasta = NULL,
  genes.file = NULL,
  annots.file = NULL,
  annots.names = NULL
)

Arguments

`groot`	path to newly created database
`fasta`	an array of names or URLs of FASTA files. Can contain wildcards for multiple files
`genes.file`	name or URL of file that contains genes. If 'NULL' no genes are imported
`annots.file`	name of URL file that contains annotations. If 'NULL' no annotations are imported
`annots.names`	annotations names

Details

This function creates a new Genomic Database at the location specified by 'groot'. FASTA files are converted to 'Seq' format and appropriate 'chrom_sizes.txt' file is generated (see "User Manual" for more details).

If 'genes.file' is not 'NULL' four sets of intervals are created in the database: tss, exons, utr3 and utr5. See gintervals.import_genes for more details about importing genes intervals.

'fasta', 'genes.file' and 'annots.file' can be either a file path or URL in a form of 'ftp://[address]/[file]'. 'fasta' can also contain wildcards to indicate multiple files. Files that these arguments point to can be zipped or unzipped.

See the 'Genomes' vignette for details on how to create a database from common genome sources.

Value

None.

Examples


ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10"
mm10_dir <- file.path(tempdir(), "mm10")
# only a single chromosome is loaded in this example
# see "Genomes" vignette how to downloaded all of them/other genomes
gdb.create(
    mm10_dir,
    paste(ftp, "chromosomes", paste0(
        "chr", c("X"),
        ".fa.gz"
    ), sep = "/"),
    paste(ftp, "database/knownGene.txt.gz", sep = "/"),
    paste(ftp, "database/kgXref.txt.gz", sep = "/"),
    c(
        "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol",
        "refseq", "protAcc", "description", "rfamAcc",
        "tRnaName"
    )
)
gdb.init(mm10_dir)
gintervals.ls()
gintervals.all()

misha documentation built on Sept. 14, 2023, 5:08 p.m.