mapUniProt: Mapping identifiers with the UniProt API
In Bioconductor/UniProt.ws: R Interface to UniProt Web Services

View source: R/mapUniProt.R

allFromKeys

R Documentation

Mapping identifiers with the UniProt API

Description

These functions are the main workhorses for mapping identifiers from one database to another. They make use of the latest UniProt API (seen at https://www.uniprot.org/help/api).

Usage

allFromKeys()

allToKeys(fromName = "UniProtKB_AC-ID")

returnFields()

mapUniProt(
  from = "UniProtKB_AC-ID",
  to = "UniRef90",
  columns = character(0L),
  query,
  verbose = FALSE,
  debug = FALSE,
  paginate = TRUE,
  pageSize = 500L
)

queryUniProt(
  query = character(0L),
  fields = c("accession", "id"),
  collapse = " OR ",
  n = Inf,
  pageSize = 25L
)

Arguments

`fromName`	`character(1)` A `from` key to use as the basis of mapping to other keys, by default, `"UniProtKB_AC-ID"`.
`from`	`character(1)` The identifier type to map from, by default "UniProtKB_AC-ID", short for UniProt accession identifiers. See a list of all 'from' type identifiers with `allFromKeys`.
`to`	`character(1)` The target mapping identifier, by default "UniRef90". It can be any one of those returned by `allToKeys` from the appropriate `fromName` argument.
`columns`, `fields`	`character()` Additional information to be retreived from UniProt service. See a full list of possible input return fields at https://www.uniprot.org/help/return_fields. Example fields include, "accession", "id", "gene_names", "xref_pdb", "xref_hgnc", "sequence", etc.
`query`	`character()` or named `list()` Typically, a string that would indicate the target accession identifiers but can also be a named list based on the available query fields. See https://www.uniprot.org/help/query-fields for a list of query fields. The typical query might only include a character vector of UniProt accession identifiers, e.g., `c("A0A0C5B5G6", "A0A1B0GTW7", "A0JNW5", "A0JP26", "A0PK11", "A1A4S6")`
`verbose`	`logical(1)` Whether the operations should provide verbose updates (default `FALSE`).
`debug`	`logical(1)` Whether to display the URL API endpoints, for advanced debugging (default `FALSE`)
`paginate`	`logical(1)` Whether to use the pagination API (i.e., "results" vs "stream") in the request responses. For performance, it is set to `TRUE` by default.
`pageSize`	`integer(1)` number of records per page. It corresponds to the `size` parameter in the API request.
`collapse`	`character(1)` A string indicating either `" OR "` or `" AND "` for combining `query` clauses.
`n`	`numeric(1)` Maximum number of rows to return

Details

Note that mapUniProt is used internally by the select method but made available for API queries with finer control. Provide values from the name column in returnFields as the columns input in either mapUniProt or select method.

When using from='Gene_Name', you may restrict the search results to a specific organism by including e.g., taxId=9606 in the query as a named list element. See examples below.

Value

mapUniProt: A data.frame of returned results
allToKeys: A sorted character vector of possible "To" keytypes based on the given "From" type
allFromKeys: A sorted character vector of possible "From" keytypes
returnFields: A data.frame of entries for the columns input in mapUniProt; see 'name' column

Author(s)

M. Ramos

Examples


mapUniProt(
    from="UniProtKB_AC-ID",
    to='RefSeq_Protein',
    query=c('P13368','Q9UM73','P97793','Q17192')
)

mapUniProt(
    from='GeneID', to='UniProtKB', query=c('1','2','3','9','10')
)

mapUniProt(
    from = "UniProtKB_AC-ID",
    to = "UniProtKB",
    columns = c("accession", "id"),
    query = list(organism_id = 10090, ids = c('Q7TPG8', 'P63318'))
)

## restrict 'from = Gene_Name' result to taxId 9606
mapUniProt(
    from = "Gene_Name",
    to = "UniProtKB-Swiss-Prot",
    columns = c("accession", "id"),
    query = list(taxId = 9606, ids = 'TP53')
)

mapUniProt(
    from = "UniProtKB_AC-ID", to = "UniProtKB",
    query = c("P31946", "P62258"),
    columns = c("accession", "id", "xref_pdb", "xref_hgnc", "sequence")
)

queryUniProt(
    query = c("accession:A5YMT3", "organism_id:9606"),
    fields = c("accession", "id", "reviewed"),
    collapse = " AND "
)

allToKeys(fromName = "UniRef100")

head(allFromKeys())

head(returnFields())

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