| geneConnector {netboxr} | R Documentation |
Generate sub-network mapping from a candidate gene list
geneConnector(
geneList,
networkGraph,
directed = FALSE,
pValueAdj = c("BH", "bonferroni"),
pValueCutoff = 0.05,
communityMethod = "lec",
keepIsolatedNodes = FALSE
)
geneList |
A vector containing candidate gene list |
networkGraph |
An igraph graph object |
directed |
TRUE of FALSE |
pValueAdj |
A string for p-value correction method c('BH, 'Bonferroni') |
pValueCutoff |
A number for p-value cutoff for linker nodes |
communityMethod |
A string for community detection method c('ebc','lec') |
keepIsolatedNodes |
logic value |
a list with four lists (i.e. netboxOutput, nodeType, moduleMembership, neighborData) netboxGraph is igraph object. netboxCommunity is igraph object. netboxOutput is a data frame. nodeType is a data frame. moduleMembership is a data frame. neighborData is a data frame.
Eric Minwei Liu, emliu.research@gmail.com
data(netbox2010)
sifNetwork<-netbox2010$network
graphReduced <- networkSimplify(sifNetwork,directed = FALSE)
geneList<-as.character(netbox2010$geneList)
results<-geneConnector(geneList=geneList,networkGraph=graphReduced,
pValueAdj='BH',pValueCutoff=0.05,
communityMethod='lec',keepIsolatedNodes=FALSE)
names(results)
plot(results$netboxGraph, layout = layout_with_fr)
write.table(results$netboxOutput,
file = "network.sif", sep = " ",
quote = FALSE, col.names = FALSE, row.names = FALSE
)
write.table(results$neighborData,
file = "neighborList.txt", sep = " ",
quote = FALSE, col.names = TRUE, row.names = FALSE
)
write.table(results$moduleMembership,
file = "memb.ebc.txt", sep = " ",
quote = FALSE, col.names = FALSE, row.names = FALSE
)
#
write.table(results$nodeType,
file = "nodeType.txt", sep = " ", quote = FALSE,
col.names = FALSE, row.names = FALSE
)
#