Descriptions of available values for columns and keytypes.
This manual page enumerates the kinds of data represented by the
values returned when the user calls columns or keytypes
All the possible values for columns and keytypes are listed
below. Users will have to actually use these methods to learn which
of the following possible values actually apply in their case.
GenBank accession numbers
Commonly used gene symbols
KEGG Identifiers for arabidopsis as indicated by aracyc
Aracyc enzyme names as indicated by aracyc
Chromosome (deprecated for Bioc > 3.1) For this information you should look at a TxDb or OrganismDb object and search for an appropriate field like TXCHROM, EXONCHROM or CDSCHROM. This information can also be retrieved from these objects using an appropriate range based accesor like transcripts, transcriptsBy etc.
Chromosome and starting base of associated gene (deprecated for Bioc > 3.1) For this information you should look at a TxDb or OrganismDb object and search for an appropriate field like TXSTART etc. or even better use the associated range based accessors like transcripts or transcriptsBy to get back GRanges objects.
Chromosome and ending base of associated gene (deprecated for Bioc > 3.1) For this information you should look at a TxDb or OrganismDb object and search for an appropriate field like TXEND etc. or even better use the associated range based accessors like transcripts or transcriptsBy to get back GRanges objects.
Common name
The description of the associated gene
The ensembl ID as indicated by ensembl
The ensembl protein ID as indicated by ensembl
The ensembl transcript ID as indicated by ensembl
Entrez gene Identifiers
Enzyme Commission numbers
Evidence codes for GO associations with a gene of interest
Evidence codes for GO (includes less specific terms)
The full gene name
GO Identifiers associated with a gene of interest
GO Identifiers (includes less specific terms)
InterPro identifiers
IPI accession numbers
cytoband locations
Online Mendelian Inheritance in Man identifiers
For GO Identifiers, which Gene Ontology (BP, CC, or MF)
Which Gene Ontology (BP, CC, or MF), (includes less specific terms)
Yeast ORF Identifiers
KEGG Pathway Identifiers
PFAM Identifiers
Pubmed Identifiers
Probe or manufacturer Identifiers for a chip package
Prosite Identifiers
Refseq Identifiers
Saccharomyces Genome Database Identifiers
Smart Identifiers
The official gene symbol
TAIR Identifiers
Unigene Identifiers
Uniprot Identifiers
To get the latest information about the date stamps and source URLS for the data used to make an annotation package, please use the metadata method as shown in the example below.
Unless otherwise indicated above, the majority of the data for any one package is taken from the source indicated by either it's name (if it's an org package) OR from the name of it's associated org package. So for example, org.Hs.eg.db is using "eg" in the name to indicate that most of the data in that package comes from NCBI entrez gene based data. And org.At.tair.db uses data that primarily comes from tair. For chip packages, the relevant information is the organism package that they depend on. So for example, hgu95av2.db depends on org.Hs.eg.db, and is thus primarily based on NCBI entrez gene ID information.
Marc Carlson
library(hgu95av2.db)
## List the possible values for columns
columns(hgu95av2.db)
## List the possible values for keytypes
keytypes(hgu95av2.db)
## get some values back
keys <- head(keys(hgu95av2.db))
keys
select(hgu95av2.db, keys=keys, columns=c("SYMBOL","PFAM"),
keytype="PROBEID")
## More infomation about the dates and original sources for these data:
metadata(hgu95av2.db)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.