OrganismDb objects

The OrganismDb class is a container for storing knowledge about existing Annotation packages and the relationships between these resources. The purpose of this object and it's associated methods is to provide a means by which users can conveniently query for data from several different annotation resources at the same time using a familiar interface.

The supporting methods select, columns and keys are used together to extract data from an OrganismDb object in a manner that should be consistent with how these are used on the supporting annotation resources.

The family of seqinfo style getters (seqinfo, seqlevels, seqlengths, isCircular, genome, and seqnameStyle) is also supported for OrganismDb objects provided that the object in question has an embedded TxDb object.


In the code snippets below, x is a OrganismDb object. For the metadata and show methods, there is also support for FeatureDb objects.

keytypes(x): allows the user to discover which keytypes can be passed in to select or keys and the keytype argument.
keys(x, keytype, pattern, column, fuzzy): Return keys for the database contained in the TxDb object . The keytype argument specifies the kind of keys that will be returned and is always required. If keys is used with pattern, it will pattern match on the keytype. But if the column argument is also provided along with the pattern argument, then pattern will be matched against the values in column instead. If keys is called with column and no pattern argument, then it will return all keys that have corresponding values in the column argument. Thus, the behavior of keys all depends on how many arguments are specified. Use of the fuzzy argument will toggle fuzzy matching to TRUE or FALSE. If pattern is not used, fuzzy is ignored.
columns(x): shows which kinds of data can be returned for the OrganismDb object.
select(x, keys, columns, keytype): When all the appropriate arguments are specifiedm select will retrieve the matching data as a data.frame based on parameters for selected keys and columns and keytype arguments.

See Also

  • OrganismDb-class
  • class:OrganismDb
  • OrganismDb
  • columns,OrganismDb-method
  • keytypes,OrganismDb-method
  • keys,OrganismDb-method
  • select,OrganismDb-method
  • metadata,OrganismDb-method
  • dbconn,OrganismDb-method
  • dbfile,OrganismDb-method
  • seqinfo,OrganismDb-method
## load a package that creates an OrganismDb
## then the methods can be used on this object.
columns <- columns(Homo.sapiens)[c(7,10,11,12)]
keys <- head(keys(, "ENTREZID"))
keytype <- "ENTREZID"
res <- select(Homo.sapiens, keys, columns, keytype)

## Get the DB connections or DB file paths associated with those for
## each.
Documentation reproduced from package OrganismDbi, version 1.10.0, License: Artistic-2.0

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