Using this function, you can retrieve the Smith-Waterman bit scores among proteins of the same species. Bit Scores serve as similarity scores between protein sequence; And, according to STRING documentations, as a proxy for protein homology.

rba_string_homology_intra(ids, species = NULL, ...)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional if your input is less than 100 IDs.)

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A data frame with bit scores between your supplied proteins and their self-hit. To Reduce the transferred data, STRING returns only one half of the similarity matrix; This will not pose a problem because similarity matrix is symmetrical.

Details

Note that this function will retrieve similarity scores of different proteins "within the same species". To Get a similarity scores of a given protein and it's closets homologous proteins in other species, see rba_string_homology_inter.
Similarity matrix is imported -by STRING- from: Similarity Matrix of Proteins (SIMAP)

Corresponding API Resources

"POST https://string-db.org/api/[output-format]/homology?identifiers= [your_identifiers]"

References

  • Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. PMID: 30476243; PMCID: PMC6323986.

  • STRING API Documentation

See also

Examples

# \donttest{
rba_string_homology_intra(ids = c("CDK1", "CDK2"), species = 9606)
# }