map2LL {AnnBuilder} | R Documentation |
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
map2LL(pkgName, pkgPath, organism, version, author, eg = EG(parser = file.path(.path.package("AnnBuilder"), "scripts", "egLLMappingUGParser")), lazyload = TRUE) 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")
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 |
lazyload |
lazyload a boolean indicating whether a lazy
load database will be created |
eg |
eg an EG object |
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
invisible
This function is part of Bioconductor project at Dana-Farber Cancer Institute to provide bioinfomatics functionalities through R
Jianhua Zhang
http://www.ncbi.nlm.nih.gov/LocusLink/
## Not run: # Please note that the example will take a while to finish map2LL(pkgPath = tempdir(), version = "1.0.0", organism = "human", author = list(author = "myName", maintainer = "myeail@email.com")) ## End(Not run)