Get STRINGdb PPI data

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)

Arguments

gene.cccn

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

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)
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