CHANGES IN VERSION 1.1.1 ------------------------ o remove geneID2Name, instead import EXTID2NAME from DOSE. <2012-03-12, Mon> o remove most of the codes in enrichPathway, instead import enrich.internal in DOSE. implement some S3 method for mapping. pathID2Name was rename to TERM2NAME, which will called by enrich.internal. <2012-03-12, Tue> CHANGES IN VERSION 0.99.0 ------------------------ o change package name to ReactomePA, for there is already an RPA package. <2012-03-02, Fri> o Vignette issues: <2012-03-02, Fri> change image format from .eps to .pdf, make it easier to build. remove the tolatex tag of sessionInfo(), make the output more readble. o re-implement geneID2Name using select method. <2012-03-02, Fri> o add examples in man pages. <2012-03-02, Fri> o remove man pages of internal functions. <2012-03-02, Fri> o import plot summary from stats4, for BiocGenerics (version 0.1.10) removed them <2012-03-03, Sat> o add Methods section in enrichPathwayResult-class man page. <2012-03-05, Mon> CHANGES IN VERSION 0.2.3 ------------------------ o @exportMethod plot <2012-02-15 Wed> o fix bug when calling summary method from plot, for summary defined in base is S3 method, instead import summary generic from stats4 <2012-02-15 Wed> CHANGES IN VERSION 0.2.2 ------------------------ o remove generic definition of show, summary and plot, add NAMESPACE import show from methods and plot from graphics. summary need not to import, for is defined in the base package <2012-02-10 Fri> CHANGES IN VERSION 0.2.1 ------------------------ o update vignette <2012-02-09 Thu> o add sample data (an example list of genes from ProfCom: http://webclu.bio.wzw.tum.de/profcom/gene_Lists/example1.txt the gene symbols were converted to entrezgene) <2012-02-09 Thu> CHANGES IN VERSION 0.2.0 ------------------------ o separate codes of mapping pathway ID to pathway Name to a new function pathID2Name <2012-02-09 Thu> o implement geneID2Name function for mapping gene ID to gene Symbol <2012-02-09 Thu> o add parameter readable in function enrichPathway <2012-02-09 Thu> o implement cnetplot for plotting category net <2012-02-09 Thu> o modify plot function for class enrichPathwayResult to use cnetplot <2012-02-09 Thu> CHANGES IN VERSION 0.1.1 ------------------------ o add vignette <2012-02-08 Wed> o bug fixed for multiple mapping of pathway ID to pathway Name such as pathway 162906 can mapping to 1629061 and 1629062 when getting pathway name, remain the first one. <2012-02-08 Wed> CHANGES IN VERSION 0.1.0 ------------------------ o implement show, summary and plot method for enrichPathwayResult class <2012-02-08 Wed> o define class enrichPathwayResult to store result of enrichPathway <2012-02-08 Wed> o implement enrichPathway function for enrichment analysis. using hypergeometric model <2012-02-08 Wed> o initial package skeleton <2012-02-08 Wed>