TrEMBL to SwissProt by gene names

Usage

uniprot_genesymbol_cleanup(uniprots, organism = 9606, only_trembls = TRUE)

Arguments

uniprots: Character vector possibly containing TrEMBL IDs.
organism: Character or integer: organism name or identifier.
only_trembls: Attempt to convert only known TrEMBL IDs of the organism. This is the recommended practice.

Value

Data frame with two columns: "input" and "output". The first one contains all identifiers from the input vector `uniprots`. The second one has the corresponding identifiers which are either SwissProt IDs with gene names identical to the TrEMBL IDs in the input, or if no such records are available, the output has the input items unchanged.

Details

Sometimes one gene or protein is represented by multiple identifiers in UniProt. These are typically slightly different isoforms, some of them having TrEMBL IDs, some of the SwissProt. For the purposes of most systems biology application, the most important is to identify the protein or gene in a way that we can recognize it in other datasets. Unfortunately UniProt or Ensembl do not seem to offer solution for this issue. Hence, if we find that a TrEMBL ID has a gene name which is also associated with a SwissProt ID, we replace this TrEMBL ID by that SwissProt. There might be a minor difference in their sequence, but most of the omics analyses do not even consider isoforms. And it is quite possible that later UniProt will convert the TrEMBL record to an isoform within the SwissProt record. Typically this translation is not so important (but still beneficial) for human, but for other organisms it is critical especially when translating from foreign identifiers.

This function accepts a mixed input of UniProt IDs and provides a distinct translation table that you can use to translate your data.

Examples

if (FALSE) {
uniprot_genesymbol_cleanup('Q6PB82', organism = 10090)
# # A tibble: 1 × 2
#   input  output
#   <chr>  <chr>
# 1 Q6PB82 O70405
}