UniProt.ws-methods: UniProt.ws methods from AnnotationDbi

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

UniProt.ws methods from AnnotationDbi

Description

Various methods from AnnotationDbi such as select, columns, keys, keytypes, and species are made available for UniProt.ws objects.

Usage

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

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

## S4 method for signature 'UniProt.ws'
keys(x, keytype)

## S4 method for signature 'UniProt.ws'
select(x, keys, columns, keytype, ...)

Arguments

x	a UniProt.ws object.
keytype	character(1) 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
keys	character() the keys to select records for from the database. All possible keys are returned by using the keys method.
columns	character() 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.
...	Additional arguments passed to lower level functions, mainly used for the to input to mapUniProt.

Details

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.

Value

• keys,columns,keytypes, return a character vector of possible values

  • select returns a data.frame

Functions

• keytypes(UniProt.ws): Get keytypes for a UniProt.ws object

• columns(UniProt.ws):

• keys(UniProt.ws): Get keys for a UniProt.ws object

• select(UniProt.ws): Select columns from keys

See Also

UniProt.ws

Examples

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

## 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 Jan. 5, 2025, 9:24 a.m.