uniprot_full_id_mapping_table {OmnipathR} | R Documentation

## Creates an ID translation table from UniProt data

### Description

Creates an ID translation table from UniProt data

### Usage

    uniprot_full_id_mapping_table(
      to,
      from = "id",
      reviewed = TRUE,
      organism = 9606
    )

### Arguments

`to` | Character or symbol: target ID type. See Details for possible values.
`from` | Character or symbol: source ID type. See Details for possible values.
`reviewed` | Translate only reviewed (`TRUE`), only unreviewed (`FALSE`) or both (`NULL`) UniProt records.
`organism` | Integer, NCBI Taxonomy ID of the organism (by default 9606 for human).

### Details

For both source and target ID type, this function accepts column codes used by UniProt and some simple shortcuts defined here. For the UniProt codes please refer to https://www.uniprot.org/help/uniprotkb The shortcuts are entrez, genesymbol, genesymbol_syn (synonym gene symbols), hgnc, embl, refseqp (RefSeq protein), enst (Ensembl transcript), uniprot_entry (UniProtKB AC, e.g. EGFR_HUMAN), protein_name (full name of the protein), uniprot (UniProtKB ID, e.g. P00533). For a complete table please refer to `translate_ids`.

### Value

A data frame (tibble) with columns 'From' and 'To', UniProt IDs and the corresponding foreign IDs, respectively.

### See Also

`translate_ids`

### Examples

    uniprot_entrez <- uniprot_full_id_mapping_table(to = 'entrez')
    uniprot_entrez
    # # A tibble: 20,723 x 2
    #    From   To
    #    <chr>  <chr>
    #  1 Q96R72 NA
    #  2 Q9UKL2 23538
    #  3 Q9H205 144125
    #  4 Q8NGN2 219873
    #  5 Q8NGC1 390439
    # # . with 20,713 more rows

[Package OmnipathR version 3.0.0 Index]