UniProtWS-class: UniProt.ws objects and their related methods and functions

In Bioconductor/UniProt.ws: R Interface to UniProt Web Services

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)
  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
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 of possible columns
head(columns(up))

## list all possible keys of type entrez gene ID
egs <- keys(up, "GeneID")

## use select to extract some data
res <- select(
    x = up,
    keys = c("22627","22629"),
    columns = c("xref_pdb","xref_hgnc","sequence"),
    keytype = "GeneID"
)
res

univals <- c("A0A0C5B5G6", "A0A1B0GTW7", "A0JNW5", "A0JP26", "A0PK11")
res <- select(
    x = up,
    keys = univals,
    to = "Ensembl"
)
res

Bioconductor/UniProt.ws documentation built on Oct. 29, 2023, 5:02 p.m.