Question: Re: metaData
gravatar for John Zhang
15.7 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
New versions of annotation data packages have been put on the web for downloading. Please let me know if there is any problem. New features include: 1. Values for the GO environment of platform specific package (e. g. hgu95av2GO) now is a list that contains sub lists. Names of the list are the GO ids corresponding to a probe id and each element of the sub lists has three elements named "GOID", "Evidence", and "Ontology" for GO id, evidence code and ontology (MF, BP, CC). For example: > library(hgu95av2) > lookUp(ls(hgu95av2GO)[25], "hgu95av2", "GO") $"GO:0005126" $"GO:0005126"$GOID [1] "GO:0005126" $"GO:0005126"$Evidence [1] "TAS" $"GO:0005126"$Ontology [1] "MF" $"GO:0006952" $"GO:0006952"$GOID [1] "GO:0006952" $"GO:0006952"$Evidence [1] "IEA" $"GO:0006952"$Ontology [1] "BP" $"GO:0005576" $"GO:0005576"$GOID [1] "GO:0005576" $"GO:0005576"$Evidence [1] "IEA" $"GO:0005576"$Ontology [1] "CC" 2. The GO package has two new environments GOGO2LL and GOLL2GO and the GOTERM environment contains GO terms for all the three (MF, BP, CC) categories with the terms named by MF, BP, or CC. 3. The KEGG package has KEGGEXTID2PATHID and KEGGPATHID2EXTID environments with mappings/reverser mappings between pathway ids and external ids. External ids are LocusLink ids for human, mouse, and rat and ORF for yeast.
annotation go yeast probe • 547 views
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