string_links {WGCNA} R Documentation

locate the STRING protein interaction data files inside a STRING database

Description

folder and attach them to the GRN pipeline options.

Usage

string_links(opts, string.db);

Arguments

opts

the GRN pipeline options object (usually created via new("GRN_opts", ...) and possibly piped through other option helpers). This function mutates and returns the same options object. [as GRNBuildOptions]

string.db

the directory of the extracted STRING database files (for example K:\hsa_grn\string-db). The links file is picked with the priority: compact 9606.protein.links.v*.txt (3 columns) > detailed version > any other *protein.links*.txt; the .gz archives and the physical-subset files are always skipped. The aliases file (*protein.aliases*.txt) is located as well and used to build the Ensembl gene id => STRING protein id mapping automatically. [as string]

Details

STRING protein interactions are used by the GRN pipeline in two configurable ways: as a confidence re-weighting evidence for the existing co-expression edges, and/or as a topology completion source that adds the protein interaction pairs missing in the co-expression network (see GRN_opts fields stringAddEdges, stringMinScore and stringWeight).

Authors

TRNtoolkit

Value

the same GRNBuildOptions object with the stringLinks and stringAliases file paths filled in. When no links file is found, the STRING protein interaction evidence is disabled (a warning is printed).

clr value class

Examples

 let opts = new("GRN_opts", minAbsCorrelation = 0.3, enableGpu = TRUE)
 |> string_links(string_db = "K:\hsa_grn\string-db");
[Package WGCNA version 1.0.0.0 Index]