The STRING database provides a resource for known and predicted protein-protein interactions. The type of interactions include direct (physical) and indirect (functional) interactions. Through the R package STRINGdb this resource if provided to R users. This function provides a convenient wrapper for STRINGdb functions that allow an easy use within the protti pipeline.

analyse_functional_network(
  data,
  protein_id,
  string_id,
  organism_id,
  score_threshold = 900,
  binds_treatment = NULL,
  halo_color = NULL,
  plot = TRUE
)

Arguments

data

a data frame that contains significantly changing proteins (STRINGdb is only able to plot 400 proteins at a time so do not provide more for network plots). Information about treatment binding can be provided and will be displayed as colorful halos around the proteins in the network.

protein_id

a character column in the data data frame that contains the protein accession numbers.

string_id

a character column in the data data frame that contains STRING database identifiers. These can be obtained from UniProt.

organism_id

a numeric value specifying an organism ID (NCBI taxon-ID). This can be obtained from here. H. sapiens: 9606, S. cerevisiae: 4932, E. coli: 511145.

score_threshold

a numeric value specifying the interaction score that based on STRING has to be between 0 and 1000. A score closer to 1000 is related to a higher confidence for the interaction. The default value is 900.

binds_treatment

a logical column in the data data frame that indicates if the corresponding protein binds to the treatment. This information can be obtained from different databases, e.g UniProt.

halo_color

optional, character value with a color hex-code. This is the color of the halo of proteins that bind the treatment.

plot

a logical that indicates whether the result should be plotted or returned as a table.

Value

A network plot displaying interactions of the provided proteins. If binds_treatment was provided halos around the proteins show which proteins interact with the treatment. If plot = FALSE a table with interaction information is returned.

Examples

# \donttest{ # Create example data data <- data.frame( uniprot_id = c( "P0A7R1", "P02359", "P60624", "P0A7M2", "P0A7X3", "P0AGD3" ), database_string = c( "511145.b4203;", "511145.b3341;", "511145.b3309;", "511145.b3637;", "511145.b3230;", "511145.b1656;" ), is_known = c( TRUE, TRUE, TRUE, TRUE, TRUE, FALSE ) ) # Perform network analysis network <- analyse_functional_network( data, protein_id = uniprot_id, string_id = database_string, organism_id = 511145, binds_treatment = is_known, plot = TRUE )
#> [1] "Parameter add_link not available in version 11.0 (please use 11.0b or later)"
network
#> NULL
# }