cleanSrcObjs {AnnBuilder}R Documentation

Supporting function that may no of any other usese

Description

Functions in this group are mainly for supporting purposes and may not be of any use outside the package they reside

Usage

getRepSourceNBuilt(name, object)
mapGO2Probe(ll, baseMapType)
writeReverseMap(annData, pkgName, pkgPath)
writeAnnData2Pkg(annData, pkgName, pkgPath)
getAnnData(srcObjs)
getUniMappings(baseName, ll, 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),
llUrl = getSrcUrl("ll"), 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) 

Arguments

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
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

Author(s)

Jianhua Zhang


[Package AnnBuilder version 1.4.21 Index]