benchmark_ppi_pathway_view {STRINGdb}R Documentation

benchmark_ppi_pathway_view

Description

Takes in input the results of the benchmark_ppi function, and constructs a new table that provides a view at the pathway level (i.e. it list all the pathways to which the interactions belong)

Usage

## S4 method for signature 'STRINGdb'
benchmark_ppi_pathway_view(benchmark_ppi_data_frame, precision_threshold=0.2, pathwayType = "KEGG")

Arguments

benchmark_ppi_data_frame

data frame that comes out from the benchmark_ppi function.

precision_threshold

threshold that specify where to stop taking considering the interactions in the sorted input data frame (the list is scanned until the precision goes below this value).

pathwayType

the pathway category to use (KEGG by default)

Value

data frame containing the pathways (i.e. terms) of the input proteins. Several parameters are reported: pathway coverage (i.e. number of interactions in the list belonging to the pathway / maximum number of interactions between the pathay proteins (i.e. proteins * (proteins-1)/2 ) ) total_representation (i.e. number of interactions in the list belonging to the pathway / size of the input data frame )

Author(s)

Andrea Franceschini


[Package STRINGdb version 1.24.0 Index]