translate_ids: Translate gene, protein and small molecule identifiers
In saezlab/OmnipathR: OmniPath web service client and more

translate_ids

R Documentation

Translate gene, protein and small molecule identifiers

Description

Translates a vector of identifiers, resulting a new vector, or a column of identifiers in a data frame by creating another column with the target identifiers.

Usage

translate_ids(
  d,
  ...,
  uploadlists = FALSE,
  ensembl = FALSE,
  hmdb = FALSE,
  ramp = FALSE,
  chalmers = FALSE,
  entity_type = NULL,
  keep_untranslated = TRUE,
  return_df = FALSE,
  organism = 9606,
  reviewed = TRUE,
  complexes = NULL,
  complexes_one_to_many = NULL,
  track = FALSE,
  inspect = FALSE,
  inspect_grp = NULL,
  expand = TRUE
)

Arguments

`d`	Character vector or data frame.
`...`	At least two arguments, with or without names. The first of these arguments describes the source identifier, the rest of them describe the target identifier(s). The values of all these arguments must be valid identifier types as shown in Details. The names of the arguments are column names. In case of the first (source) ID the column must exist. For the rest of the IDs new columns will be created with the desired names. For ID types provided as arguments without names, the name of the ID type will be used for column name.
`uploadlists`	Force using the `uploadlists` service from UniProt. By default the plain query interface is used (implemented in `uniprot_full_id_mapping_table` in this package). If any of the provided ID types is only available in the uploadlists service, it will be automatically selected. The plain query interface is preferred because in the long term, with caching, it requires less download and data storage.
`ensembl`	Logical: use data from Ensembl BioMart instead of UniProt.
`hmdb`	Logical: use HMDB ID translation data.
`ramp`	Logical: use RaMP ID translation data.
`chalmers`	Logical: use ID translation data from Chalmers Sysbio GEM.
`entity_type`	Character: "gene" and "smol" are short symbols for proteins, genes and small molecules respectively. Several other synonyms are also accepted.
`keep_untranslated`	In case the output is a data frame, keep the records where the source identifier could not be translated. At these records the target identifier will be NA.
`return_df`	Return a data frame even if the input is a vector.
`organism`	Character or integer, name or NCBI Taxonomy ID of the organism (by default 9606 for human). Matters only if `uploadlists` is `FALSE`.
`reviewed`	Translate only reviewed (`TRUE`), only unreviewed (`FALSE`) or both (`NULL`) UniProt records. Matters only if `uploadlists` is `FALSE`.
`complexes`	Logical: translate complexes by their members. Only complexes where all members can be translated will be included in the result. If `NULL`, the option `omnipathr.complex_translation` will be used.
`complexes_one_to_many`	Logical: allow combinatorial expansion or use only the first target identifier for each member of each complex. If `NULL`, the option `omnipathr.complex_translation_one_to_many` will be used.
`track`	Logical: Track the records (rows) in the input data frame by adding a column `record_id` with the original row numbers.
`inspect`	Logical: inspect the mappings for each ID for ambiguity. If TRUE, for each translated column, a new column will be inculded with values `one-to-one`, `one-to-many`, `many-to-one` or `many-to-many`.
`inspect_grp`	Character vector: additional column names to group by during inspecting ambiguity. By default, the identifier columns (from and to) will be used to determine the ambiguity of mappings.
`expand`	Logical: if `TRUE`, ambiguous (to-many) mappings will be expanded to multiple rows, resulting character type columns; if `FALSE`, the original rows will be kept intact, and the target columns will be lists of character vectors.

Details

This function, depending on the uploadlists parameter, uses either the uploadlists service of UniProt or plain UniProt queries to obtain identifier translation tables. The possible values for from and to are the identifier type abbreviations used in the UniProt API, please refer to the table here: https://www.uniprot.org/help/api_idmapping. In addition, simple synonyms are available which realize a uniform API for the uploadlists and UniProt query based backends. These are the followings:

OmnipathR	Uploadlists	UniProt query	Ensembl BioMart
uniprot	ACC	id	uniprotswissprot
uniprot_entry	ID	entry name
trembl	reviewed = FALSE	reviewed = FALSE	uniprotsptrembl
genesymbol	GENENAME	genes(PREFERRED)	external_gene_name
genesymbol_syn		genes(ALTERNATIVE)	external_synonym
hgnc	HGNC_ID	database(HGNC)	hgnc_symbol
entrez	P_ENTREZGENEID	database(GeneID)
ensembl	ENSEMBL_ID		ensembl_gene_id
ensg	ENSEMBL_ID		ensembl_gene_id
enst	ENSEMBL_TRS_ID	database(Ensembl)	ensembl_transcript_id
ensp	ENSEMBL_PRO_ID		ensembl_peptide_id
ensgg	ENSEMBLGENOME_ID
ensgt	ENSEMBLGENOME_TRS_ID
ensgp	ENSEMBLGENOME_PRO_ID
protein_name		protein names
pir	PIR	database(PIR)
ccds		database(CCDS)
refseqp	P_REFSEQ_AC	database(refseq)
ipro			interpro
ipro_desc			interpro_description
ipro_sdesc			interpro_short_description
wikigene			wikigene_name
rnacentral			rnacentral
gene_desc			description
wormbase		database(WormBase)
flybase		database(FlyBase)
xenbase		database(Xenbase)
zfin		database(ZFIN)
pbd	PBD_ID	database(PDB)	pbd

For a complete list of ID types and their synonyms, including metabolite and chemical ID types which are not shown here, see id_types.

The mapping between identifiers can be ambiguous. In this case one row in the original data frame yields multiple rows or elements in the returned data frame or vector(s).

Value

Data frame: if the input is a data frame or the input is a vector and return_df is TRUE.
Vector: if the input is a vector, there is only one target ID type and return_df is FALSE.
List of vectors: if the input is a vector, there are more than one target ID types and return_df is FALSE. The names of the list will be ID types (as they were column names, see the description of the ... argument), and the list will also include the source IDs.

Examples

d <- data.frame(
    uniprot_id = c(
        'P00533', 'Q9ULV1', 'P43897', 'Q9Y2P5',
        'P01258', 'P06881', 'P42771', 'Q8N726'
    )
)
d <- translate_ids(d, uniprot_id = uniprot, genesymbol)
d
#   uniprot_id genesymbol
# 1     P00533       EGFR
# 2     Q9ULV1       FZD4
# 3     P43897       TSFM
# 4     Q9Y2P5    SLC27A5

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.