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 1.22.0 Index]