STRINGdb-class: Class '"STRINGdb"'

In STRINGdb: STRINGdb (Search Tool for the Retrieval of Interacting proteins database)

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):

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

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plot_network(string_ids, payload_id, required_score):

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

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

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load():

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get_term_proteins(term_ids, string_ids, enableIEA):

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get_summary(string_ids):

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get_subnetwork(string_ids):

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

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get_ppi_enrichment(string_ids):

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get_proteins():

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

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get_neighbors(string_ids):

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get_link(string_ids, required_score, network_flavor, payload_id):

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get_interactions(string_ids):

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get_homologs_besthits(string_ids, symbets, target_species_id, bitscore_threshold):

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get_homologs(string_ids, target_species_id, bitscore_threshold):

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get_graph():

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get_enrichment(string_ids, category, methodMT, iea):

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get_clusters(string_ids, algorithm):

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get_annotations_desc():

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get_annotations():

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load_all():

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initialize(...):

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add_proteins_description(screen):

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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")

Example output

Class "STRINGdb" [package "STRINGdb"]

Slots:
                  
Name:       .xData
Class: environment

Extends: 
Class "envRefClass", directly
Class ".environment", by class "envRefClass", distance 2
Class "refClass", by class "envRefClass", distance 2
Class "environment", by class "envRefClass", distance 3, with explicit coerce
Class "refObject", by class "envRefClass", distance 3

STRINGdb documentation built on March 10, 2021, 2 a.m.