qunet2xml {QUBIC} | R Documentation |
This function can convert the constructed co-expression networks into XGMML format, which can be used to do further network analysis in Cytoscape, Biomax and JNets.
qunet2xml(net, minimum = 0.6, color = cbind(grDevices::rainbow(length(net[[2]]) - 1), "gray"))
net |
Result of |
minimum |
cutoff, default: 0.6 |
color |
default: cbind(grDevices::rainbow(length(net[[2]]) - 1), 'gray') |
Text of XGMML
# Load microarray matrix data(BicatYeast) res <- biclust::biclust(BicatYeast[1:50, ], method=BCQU(), verbose = FALSE) # Get all biclusters net <- qunetwork(BicatYeast[1:50, ], res, group = c(4, 13), method = 'spearman') # Save the network to a XGMML file sink('tempnetworkresult.gr') qunet2xml(net, minimum = 0.6, color = cbind(grDevices::rainbow(length(net[[2]]) - 1), 'gray')) sink() # You can use Cytoscape, Biomax or JNets open file named tempnetworkresult.gr