UniProt.ws-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.

Usage

UniProt.ws(taxId = 9606, ...)

## S4 method for signature 'UniProt.ws'
show(object)

## S4 method for signature 'UniProt.ws'
taxId(x)

availableUniprotSpecies(pattern = "")

lookupUniprotSpeciesFromTaxId(taxId)

## S4 replacement method for signature 'UniProt.ws'
taxId(x) <- value

## S4 method for signature 'UniProt.ws'
species(object)

Arguments

taxId	numeric(1) a taxonomy identifier
...	other arguments
x, object	a UniProt.ws object.
pattern	character string containing a regular expression (or character string for fixed = TRUE) to be matched in the given character vector. Coerced by as.character to a character string if possible. If a character vector of length 2 or more is supplied, the first element is used with a warning. Missing values are allowed except for regexpr, gregexpr and regexec.
value	numeric(1) the new taxId to set

Details

UniProt.ws is a class that is used to interact with the UniProt web services. It makes use of AnnotationDbi methods similarly to AnnotationDb objects.

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.

Value

• species and lookupUniprotSpeciesFromTaxId each return a character vector of possible values

  • taxId returns a numeric value that corresponds to the taxonomy ID

  • availableUniprotSpecies returns a data.frame

Functions

• show(UniProt.ws): Show method for UniProt.ws objects

• taxId(UniProt.ws): Get the taxonomy ID from a UniProt.ws object

• taxId(UniProt.ws) <- value: Set or chnage the taxonomy ID for a UniProt.ws object

• species(UniProt.ws): Get the species name from a UniProt.ws object

Author(s)

Marc Carlson

See Also

UniProt.ws-methods

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

Bioconductor/UniProt.ws documentation built on Jan. 5, 2025, 9:24 a.m.