chrLocPkgBuilder {AnnBuilder}R Documentation

A function to build a data package containing mappings between LocusLink ids and the chromosomal locations of genes represented by the LocusLink ids

Description

This function uses data provided by UCSC to build a data package that contains mappings between LocusLink ids and chromosome numbers and the chromosomal location of genes represented by LocusLink ids on each chromosome

Usage

chrLocPkgBuilder(pkgName = "humanCHRLOC", pkgPath, version, author,
organism = "Homo sapiens", url = getSrcUrl("gp", organism))
getChrNum(chr)
saveCytoband(pkgName, pkgPath, organism, url, ext = "cytoBand.txt.gz")
getChroms4Org(organism)

Arguments

pkgName pkgName a character string for the name of the data package to be created
pkgPath pkgPath a character string for the directory where the created data package will be stored
version version a character string for the version number of the data package to be created
author author a list with an author element for the name of the creater of the data package and a maintainer element for the email address of the creater
organism organism a character string for the organism of concern
url url a character string of the url of UCSC ftp site where to file refLink.txt.gz and refGene.txt.gz are stored. The files will be used to produce the data package
chr chr a character string for the chromosome number extracted from the source data
ext ext a character string for the file name to be appanded to the argument url

Details

The data package created maps LocusLink ids to chromosomal locations. Mappings of other public data repository ids including Gene Ontology, RefSeq, and UniGene to LocusLink ids can be made available using map2LL

Value

invisible

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institue to provide bioinfomatics functionalities through R

Author(s)

Jianhua Zhang

References

See Also

map2LL

Examples

# Please note that the example will take a while to finish
if(interactive()){
chrLocPkgBuilder(pkgName = "humanCHRLOC", pkgPath = tempdir(),
version = "1.0.1", author = list(author = "who", maintainer =
"who@email.com"), organism = "human", url = getSrcUrl("gp", "human"))
}

[Package AnnBuilder version 1.4.21 Index]