athPkgBuilder {AnnBuilder}R Documentation

Functions that build annotation packages for Arbidopsis

Description

These functions are implemented specifically for building annotation data pckages for arabidopsis using the Arabidopsis information source (TAIR).

Usage

athPkgBuilder(baseName, pkgName, pkgPath, fileExt = list(estAssign =
"Genes/est_mapping/est.Assignment.Locus", seqGenes =
"Genes/TAIR_sequenced_genes", go =
"Genes/Gene_Ontology/ATH_GO_GOSLIM.20040918.txt", aliases =
"Genes/gene_aliases.20031113", pathway =
"Pathways/aracyc_dump_20040520.txt", pmid =
"Genes/Gene_Anatomy/ATH_Anatomy.20040209.txt"), ncols = list(estAssign =
7, seqGenes = 4, go = 12, aliases = 4, pathway = 4, pmid = 15),
cols2Keep = list(estAssign = c(3, 6, 7), seqGenes = c(1, 3), go = c(1,
5, 9), aliases = c(1, 2), pathway = c(1, 3, 4), pmid = c(6, 11)),
colNames = list(estAssign = c("CHRLOC", "ORI", "ACCNUM"), seqGenes =
c("ACCNUM", "CHR"), go = c("ACCNUM", "GO", "EVID"), aliases =
c("ACCNUM", "SYMBOL"), pathway = c("PATH", "ENZYME", "ACCNUM"), pmid =
c("PMID", "ACCNUM")), version = "1.1.0", makeXML = TRUE, author =
list(author = "who", maintainer = "who@email.com"), baseUrl =
"ftp://tairpub:tairpub@ftp.arabidopsis.org/home/tair/")
getOneMap(map, keyCol)
procPMIDData(pmid)
getSrcObjs4Ath()
readAthData(baseUrl, ext, col2Keep, colNames, ncols)
mergeDupMatByFirstCol(dupMat, sep = ";")

Arguments

baseName baseName a character string for the name of the base file to be used to build an annotation data package. The base file is assumed to have two columns with the first one being probe ids and second one being the corresponding TAIR locus ids.
pkgName pkgName a character string for the name of the data package to be built
pkgPath pkgPath a character string for the path to a directory where the data package to be built will be stored
fileExt fileExt a list of character strings for the extension to be appended to a base url to form a complete url for a desired source data file stored at TAIR's ftp site. Some of the names given as default will change with time and need to be updated
ncols ncols an integer indicating the total number of columns of a given source data file
cols2Keep cols2Keep a vector of integers indicating which of the columns of a given source data file will be retained when the source file is read
colNames colNames a vector of character strings for the names of the columns of the source file to be retained
version version a character string for the version number of the data package to be built
makeXML makeXML a boolean indicating whether an XML version of the data contained in the annotation data package will be created
author author a list of character stirngs with an author and maintainer element for the name and email address of the author
baseUrl baseUrl a character string for the base url to TAIRs ftp site, The default is ftp://tairpub:tairpub@ftp.arabidopsis.org/home/tair/
map map a matrix containing mappings between probe ids and annotation data
keyCol keyCol an integer or character string for the name of the column in a matrix that contains the keys based on which data in the other columns will be merged for duplicated keys
pmid pmid a matrix containing mappings between probe ids and PubMed ids regarding genes represented by the probe ids
ext ext a single string version of fileExt
dupMat dupMat a matrix with duplicating values for entries in a column defined as keys
sep sep a character string for separator to be used when values in a matrix are merged based on keys contained in another columns
col2Keep col2Keep a vector of integers indicating which of the column of a data file will be kept when a file is read

Details

The annotation data will be extracted from various sources that may change in both names and contents. The default values provided were correct at the time of implementation but may need updating when the function is actually used.

Value

The main function athPkgBuilder returns invisible()

Author(s)

Jianhua Zhang

References

http://www.arabidopsis.org

See Also

ABPkgBuilder

Examples

# No example is provided due to the length of time required to build a package

[Package AnnBuilder version 1.4.21 Index]