Use of createSimpleBimap
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Mark Dunning ★ 1.1k
@mark-dunning-3319
Last seen 3 months ago
Sheffield, Uk
Hi all, I am interested in adding some custom fields to my existing illumina annotation packages (basically extra information that we have gathered by re-annotating the probes). I have already created sqlite objects for the new data I intend to add. I thought that the createSimpleBimap function in AnnotationDbi might be an easy way to achieve this. However, I'm a little confused by the example in the SQLForge vignette: hgu95av2NAMESYMBOL <- createSimpleBimap("gene_info","gene_name","symbol",hgu95av2.db:::datac ache,"NAMESYMBOL","hgu95av2.db") This example runs fine, but I'm struggling trying to work out what is going on. Specifically, what is 'gene_info' are where does it get these data from? My guess was that it would be a table somewhere in the datacache object but it doesn't appear in the listing > tmpcon = get("dbconn", hgu95av2.db:::datacache) > dbListTables(tmpcon) [1] "accessions" "map_counts" "map_metadata" "metadata" "probes" [6] "sqlite_stat1" Regards, Mark
hgu95av2 AnnotationDbi hgu95av2 AnnotationDbi • 571 views
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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 16 months ago
United States
Hi Mark, here's one from IlluminaHumanMethylation450k.db, where the probes have two designs; from zzz.R, declaring that the map 'DESIGN' should map primary key 'Probe_ID' to field 'Infinium_Design_Type' found in table 'probedesign', in order to process them correctly: IlluminaHumanMethylation450kDESIGN <- createSimpleBimap("probedesign","Probe_ID","Infinium_Design_Type",data cache,"DESIGN","IlluminaHumanMethylation450k.db") where the schema for table 'probedesign' is like so: sqlite> .sch probedesign CREATE TABLE "probedesign"( row_names INT, Probe_ID TEXT, Infinium_Design_Type TEXT, AddressA_ID INT, AddressB_ID INT, Color_Channel, Random_Loci, Methyl27_Loci, Is_HMM_Island, NuID TEXT, CpGs INT, Coordinate_37 INT, Chromosome_37 TEXT, Coordinate_36 INT, Chromosome_36 TEXT, Genome_Build INT ); CREATE INDEX Dchannel ON probedesign(Color_Channel); CREATE INDEX Ddesign ON probedesign(Infinium_Design_Type); Hope this helps. Some of the darker incantations are up to Marc Carlson's SQLforge though... there are things about magical namespace exports that I still don't understand. --t On Thu, Mar 10, 2011 at 9:02 AM, Mark Dunning <mark.dunning@gmail.com>wrote: > Hi all, > > I am interested in adding some custom fields to my existing illumina > annotation packages (basically extra information that we have gathered > by re-annotating the probes). I have already created sqlite objects > for the new data I intend to add. I thought that the createSimpleBimap > function in AnnotationDbi might be an easy way to achieve this. > However, I'm a little confused by the example in the SQLForge > vignette: > > hgu95av2NAMESYMBOL <- > > createSimpleBimap("gene_info","gene_name","symbol",hgu95av2.db:::dat acache,"NAMESYMBOL","hgu95av2.db") > > This example runs fine, but I'm struggling trying to work out what is > going on. Specifically, what is 'gene_info' are where does it get > these data from? My guess was that it would be a table somewhere in > the datacache object but it doesn't appear in the listing > > > tmpcon = get("dbconn", hgu95av2.db:::datacache) > > dbListTables(tmpcon) > [1] "accessions" "map_counts" "map_metadata" "metadata" "probes" > [6] "sqlite_stat1" > > Regards, > > Mark > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
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