chrLocPkgBuilder {AnnBuilder} | R Documentation |
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
chrLocPkgBuilder(pkgName = "humanCHRLOC", pkgPath, version, author, organism = "Homo sapiens") getChrNum(chr) saveCytoband(pkgName, pkgPath, organism, url, ext = "cytoBand.txt.gz") getChroms4Org(organism)
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 |
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
invisible
Jianhua Zhang
# 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") }