EG-class {AnnBuilder}R Documentation

Class "EG" handles data provided by Entrez Gene

Description

Entrez Gene contains data that were previously provided by LocusLink. The EG class represents objects that contains the needed information for gettting and processing the data

Objects from the Class

Objects can be created by calls of the form new("EG", ...). A constructor (EG is available and should be used to instantiate objects of EG

Slots

accession:
Object of class "character" for the name of the file containing mappings between GenBank accession numbers and Gene ids
info:
Object of class "character" for the name of the file containing mappings between Gene ids and symbol, chromosome number for genes, cytoband information, and gene name
go:
Object of class "character" for the name of the file containing mappings between Gene ids and GO information
pubmed:
Object of class "character" for the name of the file containing mappings between Gene ids and PubMed ids
refseq:
Object of class "character" for the name of the file containing mappings between Gene ids and RefSeq ids
unigene:
Object of class "character" for the name of the file containing the mappings between Gene ids and UniGene ids
mim:
Object of class "character" for the name of the file containing mappings between Gene ids and OMIM ids
srcUrl:
Object of class "character" for the root URL where the aforementioned files reside
parser:
Object of class "character" for the name of a Perl parser that will be used to parse the source file
baseFile:
Object of class "character" for the name of the base file that contains mappings between probe ids and a public database ids that will be used to map probe ids to annotation data contained in a source file
built:
Object of class "character" for build information of the source file
fromWeb:
Object of class "logical" for inficating whether the source file should be accessed through the web or locally

Extends

Class "pubRepo", directly.

Methods

parseData
signature(object = "EG"): A method to parse a source file using a specified parser

Author(s)

Jianhua Zhang

See Also

pubRepo-class


[Package AnnBuilder version 1.8.0 Index]