map2LL {AnnBuilder}R Documentation

A function that maps LocusLink ids to other public repository ids and vice versa

Description

This function uses data files provided by NCBI to create a data package that contains mappings between LocusLink ids and GO, RefSeq, and UniGene ids and vice versa

Usage

map2LL(pkgName, pkgPath, organism, version, author, url =
"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/")
getExten(what)
getOrgName(organism, what = c("common", "scientific"))
getReverseMapping(data, sep = ";")
saveData2Env(data, fun = splitEntry, pkgName, pkgPath, envName)
reverseMap4GO(data, sep = ";", type = c("ll2GO", "GO2LL")  )
getLL2ACC(url = paste("ftp://ftp.ncbi.nih.gov/refseq/LocusLink/",
getExten("acc"), sep = ""), organism = "human") 

Arguments

organism organism a character string for the name of the organism of interest
pkgPath pkgPath a character string for the name of 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
url url a character string for the url of NCBI's ftp site where source data are stored. Current value is ftp://ftp.ncbi.nih.gov/refseq/LocusLink/
what what a character string for the type of mapping source data (i. e. "go", "ug" ...) or description of organism name("scientific" or "short")
data data a matrix to be processed
sep sep a character string the separator used to separate data elements for a given entry
envName envName a character string for the name of the environment object to be stored in the data package to be created
fun fun the name of an R function to be called to process a data set before storing the data to an environment object
pkgName pkgName a character string for the name of data package to be created
type what a character string that should either be "ll2GO" or "GO2LL" to indicate a reverse mapping from LocusLink id to GO or vice versa

Details

Three files namely loc2go, loc2ref, and loc2UG will be used to create the mappings. The files were in ftp://ftp.ncbi.nih.gov/refseq/LocusLink/ at the time of the writing. getExten maintains names for the three files. Should any of the names been changed by the server, getExten has to be modified.

getExten and saveColSepData are supporting functions to map2LL

Value

invisible

Note

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

Author(s)

Jianhua Zhang

References

http://www.ncbi.nlm.nih.gov/LocusLink/

Examples

# Please note that the example will take a while to finish
if(interactive()){
  map2LL(pkgPath = tempdir(), version = "1.0.0", organism = "human",
author = list(author = "myName", maintainer = "myeail@email.com"))
}

[Package AnnBuilder version 1.4.21 Index]