rba_string_homology_intra {rbioapi}R Documentation

Get Similarity Scores Hits of Proteins in a Species

Description

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.

Usage

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.

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)

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.

Corresponding API Resources

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

References

See Also

rba_string_map_ids, rba_string_homology_inter

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_ppi(), rba_string_homology_inter(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples


rba_string_homology_intra(ids = c("CDK1", "CDK2"), species = 9606)



[Package rbioapi version 0.8.1 Index]