STRINGdb-class {STRINGdb} | R Documentation

## Class `"STRINGdb"`

### Description

The R package STRINGdb provides a convenient interface to the STRING protein-protein interactions database for the R/bioconductor users. Please look at the manual/vignette to get additional informationd and examples on how to use the package. STRING is a database of known and predicted protein-protein interactions. It contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. Each interaction is associated with a combined confidence score that integrates the various evidences. STRING is regularly updated , the latest version 9.05 contains information on 5 millions proteins from more than 1100 species. The STRING web interface is freely accessible at: http://string-db.org/

### Extends

All reference classes extend and inherit methods from `"envRefClass"`.

### Fields

`annotations`:

  Object of class `data.frame` ~~

`annotations_description`:

  Object of class `data.frame` ~~

`graph`:

  Object of class `igraph` ~~

`proteins`:

  Object of class `data.frame` ~~

`speciesList`:

  Object of class `data.frame` ~~

`species`:

  Object of class `numeric` ~~

`version`:

  Object of class `character` ~~

`input_directory`:

  Object of class `character` ~~

`backgroundV`:

  Object of class `vector` ~~

`score_threshold`:

  Object of class `numeric` ~~

### Methods

`set_background(background_vector)`:

  ~~

`post_payload(stringIds, colors, comments, links, iframe_urls, logo_imgF, legend_imgF)`:

  ~~

`plot_network(string_ids, payload_id, required_score)`:

  ~~

`plot_ppi_enrichment(string_ids, file, sliceWindow, edgeWindow, windowExtendedReferenceThreshold, minVal, title)`:

  ~~

`map(my_data_frame, my_data_frame_id_col_names, takeFirst, removeUnmappedRows, quiet)`:

  ~~

`load()`:

  ~~

`get_term_proteins(term_ids, string_ids, enableIEA)`:

  ~~

`get_summary(string_ids)`:

  ~~

`get_subnetwork(string_ids)`:

  ~~

`get_ppi_enrichment_full(string_ids, sliceWindow, edgeWindow, windowExtendedReferenceThreshold, growingWindowLimit)`:

  ~~

`get_ppi_enrichment(string_ids)`:

  ~~

`get_proteins()`:

  ~~

`get_png(string_ids, required_score, network_flavor, file, payload_id)`:

  ~~

`get_neighbors(string_ids)`:

  ~~

`get_link(string_ids, required_score, network_flavor, payload_id)`:

  ~~

`get_interactions(string_ids)`:

  ~~

`get_homologs_besthits(string_ids, symbets, target_species_id, bitscore_threshold)`:

  ~~

`get_homologs(string_ids, target_species_id, bitscore_threshold)`:

  ~~

`get_graph()`:

  ~~

`get_enrichment(string_ids, category, methodMT, iea)`:

  ~~

`get_clusters(string_ids, algorithm)`:

  ~~

`get_annotations_desc()`:

  ~~

`get_annotations()`:

  ~~

`load_all()`:

  ~~

`initialize(...)`:

  ~~

`add_proteins_description(screen)`:

  ~~

`add_diff_exp_color(screen, logFcColStr)`:

  ~~

`show()`:

  ~~

### Author(s)

Andrea Franceschini

### References

Franceschini, A (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. In:'Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29'.

### See Also

http://stitch-db.org

### Examples

    showClass("STRINGdb")

[Package STRINGdb version 2.4.2 Index]