ontoNW: ontoNW

In nahtan/ontoNW: Gene-Ontology Relationship Network

Description

Ontology Network. Build gene-ontology relationship static and dynamic network.

Usage

ontoNW(onto, cutoff = 0.05, pdf = T, html = T, dynamic = T)

Arguments

onto	data.frame. Includes an 'id' column with term id (e.g. G0:0008150), a 'type' colum (e.g. BP, KEGG), a 'name' column (e.g. biological_process), a 'genes' column with string of genes of the query belonging to the ontology term (e.g. IL1RL1, IL5RA, TP53), and a 'fdr' column with FDR values.
cutoff	numeric. A fdr value as cutoff threshold to plot edges/nodes below cutoff
pdf	boolean. Saves the static network as pdf.
html	boolean. Saves the dynamic network as html. Applies only if dynamic=T.
dynamic	boolean. Produce a dynamic network.

Details

Layout are lgl for static network and mds for dynamic network. Read igraph and visNetwork documentation.

Value

nodes. nodesCut. Data frames with nodes id, pval, name, and type. Cutoff applies to nodesCut.

edges. edgesCut. Data frames with edges from node, to node, and weight (p-value). Cutoff applies to edgesCut.

net. netCut. igraph object. Cutoff applies to netCut.

DynNetwork. visNetwork object and htmlwidget. Cutoff applies.

Author(s)

Nathan Lemonnier [e-mail]

Examples

onto=data.frame(id  = c("GO:0002376", "GO:0032634")
                type= c("BP","BP")
                name= c("immune system process","interleukin-5 production")
                gene= c(c(IL5RA,SMPD3,CLC,IL1RL1,CYSLTR2,ALOX15,PIK3R6), c(IL5RA,IL1RL1))
                fdr = c(0.005, 0.00005)
                )
ontoNW(onto, cutoff=0.05, dynamic=T, pdf=F, html=T)       

nahtan/ontoNW documentation built on May 8, 2019, 7:41 a.m.