plot_ppi_enrichment_graph {STRINGdb}R Documentation

plot_ppi_enrichment_graph

Description

Plots a graph showing the enrichment in protein interactions in various positions of the list of genes in input.

Usage

plot_ppi_enrichment_graph(proteins, ppi_network, file, sliceWindow, edgeWindow, windowExtendedReferenceThreshold, minVal, title, quiet)

Arguments

proteins

a vector of protein identifiers

ppi_network

an igraph object containing the protein-protein interactions' graph.

file

file where to save the graph as an image

sliceWindow

defines the interval in proteins after which to compute the enrichment, scanning the list (i.e. the resolution)

edgeWindow

size of the window that we use to compute the enrichment (i.e. the window pvalue is computed using the proteins inside this "edgeWindow")

windowExtendedReferenceThreshold

defines the size of a window at the beginning of the list. The enrichment will be computed always including the proteins in this window

title

title of the graph.

minVal

minimum value that the pvalue can assume in the log-scale graph. If the p-value is lower, we convert the value to this minimum value

quiet

if set to TRUE the method runs in quiet mode (turning off any output message)

Author(s)

Andrea Franceschini

References

Pradines JR, Farutin V, Rowley S, Dancik V. Analyzing protein lists with large networks: edge-count probabilities in random graphs with given expected degrees. J. Comput. Biol. 2005;12:113-128. Franceschini, A et al. (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. In:Nucleic Acids Res. 2013 Jan;41(Database issue)


[Package STRINGdb version 1.20.0 Index]