UniProt.ws-objects {UniProt.ws} | R Documentation

## UniProt.ws objects and their related methods and functions

### Description

`UniProt.ws` is the base class for interacting with the Uniprot web services from Bioconductor.

In much the same way as an `AnnotationDb` object allows acces to select for many other annotation packages, `UniProt.ws` is meant to allow usage of `select` methods and other supporting methods to enable the easy extraction of data from the Uniprot web services.

`select`, `columns` and `keys` are used together to extract data via an `UniProt.ws` object.

`columns` shows which kinds of data can be returned for the `UniProt.ws` object.

`keytypes` allows the user to discover which keytypes can be passed in to `select` or `keys` via the `keytype` argument.

`keys` returns keys for the database contained in the `UniProt.ws` object . By default it will return the primary keys for the database, which are UNIPROTKB keys, but if used with the `keytype` argument, it will return the keys from that keytype.

`select` will retrieve the data as a data.frame based on parameters for selected `keys` and `columns` and `keytype` arguments.

The `UniProt.ws` will be loaded whenever you load the `UniProt.ws` package. This object will be set up to retrieve information from Homo sapiens by default, but this value can be changed to any of the species supported by Uniprot. The `species` and `taxId` methods allow users to see what species is currently being accessed, and `taxId<-` allows them to change this value.

`species` shows the genus and species label currently attached to the `UniProt.ws` objects database.

`taxId` shows the NCBI taxonomy ID currently attached to the `AnnotationDb` objects database. Using the equivalently names replace method (`taxId<-`) allows the user to change the taxon ID, and the species represented along with it.

`availableUniprotSpecies` is a helper function to list out the available Species along with their official taxonomy IDs that are available by Uniprot. Because there are so many species represented at UniProt, there is also a pattern argument that can be used to restrict the range of things returned to be only those whose species names match the searth term. Please remember when using this argument that the Genus is always capitalized and the species never is.

`lookupUniprotSpeciesFromTaxId` is another helper that will look up the species of any tax ID that is supported by Uniprot.

### Usage

      columns(x)
      keytypes(x)
      select(x, keys, columns, keytype, ...)
      species(object)
      taxId(x)

      availableUniprotSpecies(pattern, n=Inf)
      lookupUniprotSpeciesFromTaxId(taxId)
      UniProt.ws(taxId, ...)

### Arguments

`x` | the `UniProt.ws` object.
`object` | the `UniProt.ws` object.
`keys` | the keys to select records for from the database. All possible keys are returned by using the `keys` method.
`columns` | the columns or kinds of things that can be retrieved from the database. As with `keys`, all possible columns are returned by using the `columns` method.
`keytype` | the keytype that matches the keys used. For the `select` methods, this is used to indicate the kind of ID being used with the keys argument. For the `keys` method this is used to indicate which kind of keys are desired from `keys`
`pattern` | A string passed in to limit the results
`n` | the maximim number of results to return.
`taxId` | a taxonomy id
`...` | other arguments

### Value

`keys`,`columns`,`keytypes`, `species` and `lookupUniprotSpeciesFromTaxId` each return a character vector of possible values.

`taxId` returns a numeric value that corresponds to the taxonomy ID.

`select` and `availableUniprotSpecies` each return a data.frame.

### Author(s)

Marc Carlson

### See Also

`select`

### Examples

    ## Make a UniProt.ws object
    up <- UniProt.ws(taxId=9606)

    ## look at the object
    up

    ## get the current species
    species(up)

    ## look up available species with their tax ids
    availableUniprotSpecies("musculus")

    ## get the current taxId
    taxId(up)

    ## look up the species that goes with a tax id
    lookupUniprotSpeciesFromTaxId(9606)

    ## set the taxId to something else
    taxId(up) <- 10090
    up

    ## list the possible key types
    head(keytypes(up))

    ## list the columns that can be retreived
    head(columns(up))

    ## list all possible keys of type entrez gene ID.
    ## (this process is not instantaneous)
    if(interactive()){
      egs = keys(up, "ENTREZ_GENE")
    }

    ## use select to extract some data
    res <- select(up,
                  keys = c("22627","22629"),
                  columns = c("PDB","HGNC","SEQUENCE"),
                  keytype = "ENTREZ_GENE")
    head(res)

[Package UniProt.ws version 2.30.0 Index]