enrichment_analysis: Perform enrichment analysis on the subnetwork
In murodzhon/PCSF: Network-based interpretation of highthroughput data

Description Usage Arguments Details Value Author(s) References See Also Examples

enrichment_analysis performs functional enrichment analysis on the subnetwork obtained by the PCSF_rand, and returns an annotated subnetwork with top 15 functional enrichments and a list of tables with a complete enrichment analysis for each cluster.

1	enrichment_analysis(subnet, mode = NULL, gene_universe)

`subnet`	A subnetwork provided by `PCSF_rand`, which is obtained by merging a multiple outputs of the PCSF with random noise added edge costs. An igraph object with edge cost and vertex prize attributes representing the total number of show ups throughout all runs.
`mode`	A binary variable to choose the method for enrichment analysis, where 0 is for EnrichR API and 1 is for topGO package.
`gene_universe`	A complete list of genes (vector of gene symbols) used as background in enrichment analysis by topGO package.

An enrichment analysis of the final subnetwork obtained by multiple runs of the PCSF (with rando noise added edge costs) is performed for functional interpretation. The subnetwork is clustered using an edge betweenness clustering algorithm from the igraph package, and for each cluster functional enrichment is done by employing either EnrichR API (Chen et al., 2013) or topGO (Alexa and Rahnenfuhrer, 2009) package that is specified by the user. Important to note that EnrichR API requires a working Internet connection to perform the enrichment. If the user does not specify which tool to use for enrichment analysis, the package employs EnrichR as a default if there is Internet connection, otherwise it uses topGO.

An interactive visualization of the final subnetwork is plotted, where the node sizes and edge widths are proportional to the frequency of show ups throughout total runs. Nodes are colored according to the cluster membership, and the top 15 functional enrichment terms are displayed in tabular format during the hover-over of the node in that cluster.

A list composed of an interactive subnetwork and a table with enrichment analysis results. An interactive subnetwork annotated with enrichment analysis can be reached by $subnet. A full list of enrichment analysis for each cluster can be reached by $enrichment.

Murodzhon Akhmedov

Chen E.Y., Christopher M.T., Yan K., Qiaonan D., Zichen W., Gabriela V.M., Neil R.C., and Avi M. (2013) Enrichr: Interactive and Collaborative Html5 Gene List Enrichment Analysis Tool. BMC Bioinformatics 14 (1). BioMed Central: 1.

Alexa A. and Rahnenfuhrer J. (2009). topGO: Enrichment Analysis for Gene Ontology. R package version 2.28.0.

PCSF_rand, plot.PCSFe

## Not run: 
library("PCSF")
data("STRING")
data("Tgfb_phospho")
terminals <- Tgfb_phospho
ppi <- construct_interactome(STRING)
subnet <- PCSF_rand(ppi, terminals, n = 10, r = 0.1, w = 2, b = 1, mu = 0.0005)
res <- enrichment_analysis(subnet)
res <- enrichment_analysis(subnet, mode=0)
## End(Not run)
## Not run: 
library(topGO)
gene_universe <- V(ppi)$name
res <- enrichment_analysis(subnet, mode=1, gene_universe)
## End(Not run)
## Not run: 
plot(res$subnet)
write.table(res$enrichment[[1]],file="cluster1_complete_enrichment.txt", 
             append = FALSE, quote = FALSE, sep ="\t", row.names=FALSE)
## End(Not run)