PAnnBuilder (version 1.36.0)

InParanoidBuilder_DB: Build Data Packages for Ortholog Protein Group

Description

This function creates a data package containing ortholog protein group between two given organisms from InParanoid.

Usage

InParanoidBuilder_DB(organism = c("Arabidopsis thaliana","Apis mellifera"),
                  prefix, pkgPath, version, author)

Arguments

organism

a string vector with two elements for the name of two organisms.

prefix

the prefix of the name of the data package to be built. (e.g. "hsaSP"). The name of builded package is prefix+".db".

pkgPath

a character string for the full path of an existing directory where the built backage will be stored.

version

a character string for the version number.

author

a list with named elements "authors" containing a character vector of author names and "maintainer" containing the complete character string for the maintainer field, for example, "Jane Doe ".

Value

• This function does not return any value.

Details

Build annotation data packages for ortholog protein gropus from InParanoid. InParanoid is a database of Eukaryotic Ortholog Groups: http://inparanoid.sbc.su.se/cgi-bin/index.cgi. InParanoidBuilder_DB employes functions writeInParanoidData_DB to parse and write data. Data files in the database will be automatically downloaded to the tmp directory, so enough space is needed for the data files. After downloading, files are parsed by perl, so perl must be installed. It may take a long time to parse database and build R package. Alternatively, we have produced diverse R packages by PAnnBuilder, and you can download appropriate package via http://www.biosino.org/PAnnBuilder.

Examples

# Set path, version and author for the package.
pkgPath <- tempdir()
version <- "1.0.0"
author <- list()
author[["authors"]] <- "Hong Li"
author[["maintainer"]] <- "Hong Li <[e-mail]>"

## It may take a long time to parse database and build R package.
# Build annotation data packages "org.HsMm.ortholog.db" for orthologs between 
# Homo sapiens and Mus musculus.
if(interactive()){
    InParanoidBuilder_DB(organism = c("Homo sapiens","Mus musculus"), 
                      prefix = "org.HsMm.ortholog", pkgPath, version, author)
}