Download Protein-Protein Interaction (PPI)

Source: R/download_PPI.R

Download the Protein-Protein Interaction (PPI) information of a STRINGdb object

getPPI(genes, string_db, anno_df)

Arguments

genes

a list, A list of genes to download the respective protein- protein interaction information

string_db

A STRINGdb object, the species of the object should match the species of genes.

anno_df

An annotation data.frame mapping STRINGdb ids to gene names, e.g. downloaded with GeDi::getAnnotation()

Value

A data.frame of Protein-Protein interactions

Examples

## Mock example showing how the data should look like

genes <- c(c("CFTR", "RALA"), c("CACNG3", "ITGA3"), c("DVL2"))
string_db <- getStringDB(9606, cache_location = FALSE)
# string_db
anno_df <- getAnnotation(string_db)
#> Warning: URL 'https://stringdb-downloads.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz': status was 'SSL peer certificate or SSH remote key was not OK'
#> Error in download.file(urlStr, temp): cannot open URL 'https://stringdb-downloads.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz'
ppi <- getPPI(genes, string_db, anno_df)
#> Error in eval(expr, envir, enclos): object 'anno_df' not found

## Example using the data available in the package
if (FALSE) {
data(macrophage_topGO_example_small,
     package = "GeDi",
     envir = environment())
string_db <- getStringDB(9606)
string_db
anno_df <- getAnnotation(string_db)
genes <- GeDi::getGenes(macrophage_topGO_example_small)
ppi <- getPPI(genes, string_db, anno_df)
}