generateSeqnames_db: Generates the seqnames.db package and database

In Bioconductor/AnnotationForge: Tools for building SQLite-based annotation data packages

Generates the seqnames.db package and database

Description

This function is used to generate the seqnames.db package and it's database from the csv files contained in the template for this package within AnnotationForge. The csv files are converted into database tables, and the DB is packaged into a new seqnames.db package.

Usage

  generateSeqnames.db(version, outdir=".")

Arguments

version	Character. Version number for the final package.
outdir	Character. Path to output directory where the package is to be placed. By default the current working directory will be used.

Details

The generateSeqnames.db function allows users to regenerate the seqnames.db package from csv sources contained in the currently installed AnnotationForge package. It is expected that the typical user will not need to use this at all, but in case they do, we have made it available. We expect that the more common use case is someone who wants to make some new chromosome conventions available for the world. It is expected that this person will more typicalyl be charitable and want to share their conventions, so they could share their .csv files with us and we would add them to AnnotationForge, install the updated package and then run this function to make a new package.

The .csv files need to be formatted the same as the ones that are currently in the template in AnnotationForge. Examples of these .csv files can be found in AnnotationForge in the "inst/seqnames-template/inst/extdata/dataFiles/" directory. Each file must be named after it's corresponding genus and species with an underscore separator and a .csv file extension. The 1st line of each file defines columns that are the names of the corresponding naming conventions. And the chromosome names are then listed below this header line such that the equivalent names for the different styles share the same row.

So for example the 1st four rows of Mus_musculus look like this (but with only one newline at the end of each row):

UCSC,NCBI,ensembl

chr1,1,1

chr2,2,2

chr3,3,3

etc.

Once you have your file ready your only need to place it in the same dir in AnnoationDbi (with the other files), install AnnotationForge, and then run this function to generate a new seqnames.db package. Of course, if you have a useful set of conventions or species to contribute, it would be best if you gave your .csv files to the Bioconductor core team so that we can add these files to the official version of AnnotationForge and so that they can occur in the official seqnames.db package.

Value

A new seqnames.db package, complete with all the latest data stored in the dataFiles subdirectory

Author(s)

Marc Carlson

Examples

## Not run: 
  generateSeqnames.db(version="1.0.0")

## End(Not run)

Bioconductor/AnnotationForge documentation built on Nov. 2, 2024, 6:30 a.m.