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Get STRINGdb PPI data

GetSTRINGdb.Rd

This function finds protein-protein interaction weights by consulting utilizing the STRINGdb database. The package STRINGdb is required for this function. To download, run:

  • if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

  • BiocManager::install("STRINGdb")

Usage

GetSTRINGdb(
  gene.cccn,
  stringdb.name = "stringdb.edges",
  nodenames.name = "nodenames"
)

Arguments

gene.cccn

A matrix showing strength of relationships between proteins using common clusters between the three distance metrics (Euclidean, Spearman, and Combined (SED))

stringdb.name

Desired name for the output STRINGdb data frame; defaults to "stringdb.edges"

nodenames.name

Desired name for list of gene names; defaults to nodenames

Value

Data frame of consisting of the network of interactions from the genes of study pulled from the STRINGdb database and a list of gene names

Details

The full example takes ~10 minutes to load, so it has been commented out and the results are displayed.

Examples

# GetSTRINGdb(ex.gene.cccn, 'ex.stringdb.edges', 'ex.nodenames')
utils::head(ex.stringdb.edges)
#>     Gene.1 Gene.2              Interaction STRINGdb.combined_score
#> 1     MYH9 PIK3R2 experimental_transferred                     216
#> 11    MYH9 ABLIM1             experimental                     167
#> 25   OXCT1 ZDHHC5             experimental                     292
#> 27 SUPT16H ZDHHC5             experimental                     292
#> 33   USP15 ZDHHC5             experimental                     292
#> 35    MYH9 ATP5PO             experimental                     192
utils::head(ex.nodenames)
#>   Gene.Names
#> 1     ABLIM1
#> 2        MET
#> 3       PKP4
#> 4       MYH9
#> 5     SEC16A
#> 6     ZDHHC5