After exporting output of WGCNA to VISANT, no network appeared
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2.8 years ago

Hello I used the WGCNA package to build a network of genes and exported it to Visant for visualization. In VisANT, I first choose clear then choose homo sapiens then file>> open>> however, the screen is still clear nothing appears

Here are the first lines of the output file

MAGED2 SLC25A40 0 M0039 0.0514251382591301

MAGED2 USP33 0 M0039 0.0926696492068202

MAGED2 PHYH 0 M0039 0.071528050421208

MAGED2 ILF3 0 M0039 0.18852391370148

MAGED2 ZNF609 0 M0039 0.116570022196881

MAGED2 SYNCRIP 0 M0039 0.0613974853295692

MAGED2 ZCCHC14 0 M0039 0.10556666442767

MAGED2 SSH2 0 M0039 0.0605315336140329

MAGED2 DNAJB12 0 M0039 0.114379019615721

MAGED2 HSD11B1 0 M0039 0.080357462316124

Here is the code for export

# Recalculate topological overlap
TOM = TOMsimilarityFromExpr(datExpr, power = 6);
# Read in the annotation file
annot = read.csv(file = "GeneAnnotation.csv");
# Select module
module = "brown";
# Select module probes
probes = names(datExpr)
inModule = (moduleColors==module);
modProbes = probes[inModule];
# Select the corresponding Topological Overlap
modTOM = TOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)
# Export the network into an edge list file VisANT can read
vis = exportNetworkToVisANT(modTOM,
file = paste("VisANTInput-", module, ".txt", sep=""),
weighted = TRUE,
threshold = 0)
R • 904 views
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I have the same issue. Do you have any suggestions?


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