newTopNetwork {RegEnrich} | R Documentation |
This function create 'TopNetwork' object using 3-column edge table.
newTopNetwork( networkEdgeTable, reg = "", directed = TRUE, networkConstruction = c("new", "COEN", "GRN"), percent = 100 )
networkEdgeTable |
a data frame of 3 columns, representing 'from.gene' ('regulators'), 'to.gene' ('targets') and 'weight', respectively. |
reg |
a vector of gene regulators. |
directed |
logical, whether the network is directed. Default is TRUE. |
networkConstruction |
the method to construct this network. Possible can be: 'COEN', coexpression network; 'GRN', gene regulatory network by random forest; 'new' (default), meaning a network provided by user, rather than infered based on the expression data. |
percent |
the percentage of edges in the original whole network. Default is 100, meaning 100% edges in whole network. |
an object of topNetwork class.
data(TFs) edge = data.frame(from = rep(TFs$TF_name[seq(3)], seq(3)), to = TFs$TF_name[11:16], weight = 0.1*(6:1)) object = newTopNetwork(edge, networkConstruction = 'new', percent = 100) object str(object)