qunet2xml: Convert newwork to XGMML

In QUBIC: An R package for qualitative biclustering in support of gene co-expression analyses

Description

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.

Usage

qunet2xml(net, minimum = 0.6,
  color = cbind(grDevices::rainbow(length(net[[2]]) - 1), "gray"))

Arguments

net	Result of qunetwork
minimum	cutoff, default: 0.6
color	default: cbind(grDevices::rainbow(length(net[[2]]) - 1), 'gray')

Value

Text of XGMML

See Also

qunetwork QUBIC

Examples

# 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

QUBIC documentation built on Nov. 8, 2020, 8:17 p.m.