Package 'pathview' - Bioconductor

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8 eg2idDetailsSpecies can be specified as either kegg code, scientific name or the common name. Scientific nameand the common name are always mapped to kegg code first. Length of species should be either 1or the same as pathway.id, if not, the same set of pathway.id will be applied to all species.Valuea named character vector, either "succeed" or "failed", indicating the download status of correspondingpathways.Author(s)Weijun Luo ReferencesLuo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integrationand visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285See Alsopathview the main function, node.info the parser,Examplesdata(demo.paths)sel.2paths=demo.paths$sel.paths[1:2]download.kegg(pathway.id = sel.2paths, species = "hsa")#pathway files should be downloaded into current working directoryeg2idMapping between Entrez Gene and other IDsDescriptionThese auxillary gene ID mappers connect Entrez Gene ID to external gene, transcript or protein IDsor vise versa.Usageeg2id(eg, category = gene.idtype.list[1:2], org = "Hs", pkg.name = NULL)id2eg(ids, category = gene.idtype.list[1], org = "Hs", pkg.name = NULL)
eg2id 9Argumentsegidscategoryorgpkg.namecharacter, input Entrez Gene IDs.character, input gene/transcript/protein IDs to be converted to Entrez Gene IDs.character, for eg2id the output ID types to map from Entrez Gene, d to bec("SYMBOL", "GENENAME"); for id2eg, the input ID type to be mappedto Entrez Gene, default to be "SYMBOL".character, the two-letter abbreviation of organism name, used to determine thegene annotation package. Default org="Hs". Only effective when pkg.name isnot NULL.character, name of the gene annotation package. This package should be oneof the standard annotation packages from Bioconductor, such as "org.Hs.eg.db".Check data(bods); bods for a full list of standard annotation packages. Youmay also use your custom annotation package built with AnnotationDbi, theBioconductor Annotation Database Interface. Default pkg.name=NULL, henceargument org should be specified.DetailsKEGG uses Entrez Gene ID as its standard gene ID. Therefore, all gene data need to be mappedto Entrez Genes when working with KEGG pathways. Function id2eg does this mapping. Onthe other hand, we frequently want to check or show gene symbols or full names instead of theless informative Entrez Gene ID when working with KEGG gene nodes, Function eg2id does thisreverse mapping. These functions are written as part of the Pathview mapper module, they areequally useful for other gene ID or data mapping tasks. The use of these functions depends on geneannotation packages like "org.Hs.eg.db", which are Bioconductor standard. IFf no such packagesnot available for your interesting organisms, you may build one with Bioconductor AnnotationDbipackage.Valuea 2- or multi-column character matrix recording the mapping between input IDs to the target IDtype(s).Author(s)Weijun Luo ReferencesLuo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integrationand visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285See Alsocpd2kegg etc the auxillary compound ID mappers, mol.sum the auxillary molecular data mapper,node.map the node data mapper function.
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