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R 2.13.0, SageBionetworksCoex 0.11, running time ~4.5 hours
 
Total number of modules is 9

Module

# of loci

black

32

blue

264

brown

243

green

39

pink

32

red

35

turquoise

1422

yellow

159

Analysis of the PC1 of each module:  
Chromosomal density maps can be found here

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