cleanSrcObjs {AnnBuilder} | R Documentation |
Functions in this group are mainly for supporting purposes and may not be of any use outside the package they reside
getRepSourceNBuilt(name, object) mapGO2Probe(eg, baseMapType) writeReverseMap(annData, pkgName, pkgPath) writeAnnData2Pkg(annData, pkgName, pkgPath) getAnnData(srcObjs) getUniMappings(baseName, eg, ug, otherSrc, baseMapType) getBaseFile(baseName) getSrcObjs(srcUrls, baseName, organism, baseMapType = c("gb", "ug", "ll", "image", "refseq", "gbNRef"), fromWeb = TRUE) cleanSrcObjs(srcObjs) mapll2PathID(srcUrl, organism, exten = "gene_map.tab") mapLLNGB(organism, pkgName, pkgPath, ugUrl = getSrcUrl("ug", organism), egUrl = paste(getSrcUrl("eg"), "gene2accession.gz"), fromWeb = TRUE) getLLNGBMap(repList, what = "ll2gb") mapUGNGB(organism, pkgName, pkgPath, ugUrl = getSrcUrl("ug", organism), llUrl = getSrcUrl("ll"), fromWeb = TRUE) getRepList4Perl(organism, ugUrl = getSrcUrl("ug", organism), llUrl = getSrcUrl("ll"), fromWeb = TRUE) getTaxid(organism)
ugUrl |
ugUrl a character string for the url to the
ftp site of UniGene |
llUrl |
llUrl a character string for the url to the ftp
site of LocusLink |
egUrl |
egUrl a character string for the url to the ftp
site of Entrez Gene |
repList |
repList a list with values to be used to replace
contents in template files |
name |
name a character string for the name a data source
to be used to build a data package |
object |
object an object that is a subclass of pubRepo |
ll |
ll an object of class LL |
ug |
ug an object of class ug |
baseMapType |
baseMapType a character string for the type
of base map (e. g. gb, ug, ll, ...) |
annData |
annData a matrix derived from source data |
pkgName |
pkgName a character string for the name of the
data package to be built |
pkgPath |
pkgPath a character string for the path where a
new package will be built |
srcObjs |
srcObjs a list containing objects of class UG,
LL, GO and so on |
baseName |
baseName a character string for the nam of a
base file to be used to build a data package |
otherSrc |
otherSrc a named vector for files contianing
mappings between probe ids and LocusLink ids obtained by other
sources |
srcUrls |
srcUrls a named vector for the urls to the
source data to be used to build data packages |
srcUrl |
srcUrl a url for a source data file to be used |
fromWeb |
fromWeb a boolean indicating whether a source
url is a real url or just the path to a locally stored file |
organism |
organism a character string for the name of the
organism of concern |
exten |
exten a character string for the extension to be
appended to the end of a given url to make the url complete |
what |
what a character string that can either be ll2gb or
gb2ll |
eg |
eg an EG object |
Jianhua Zhang