changing a gold standard to a true network
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8.3 years ago
zizigolu ★ 4.3k

I have a gold standard in Arabidopsis thaliana( genes and transcription factors) like below

TFLocus    TargetLocus    InteractionType
AT5G10140    AT1G65480    -1
AT5G11260    AT1G27480    -1
AT5G11260    AT5G53370    -1
AT5G11260    AT1G03630    -1
AT5G11260    AT1G13600    -1
AT5G11260    AT2G41670    -1
AT5G11260    AT2G05160    -1
AT5G11260    AT2G40170    -1
AT5G11260    AT1G62780    -1

I need to convert this to an adjacency matrix contains only 0 and 1 to use that as a true net in minet package to evaluate my inferred network. but I don't know how to do. if someone know please help me

Thank you

R gene-regulatory-network • 1.1k views
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What are the possible states for InteractionType? -1, 0 and 1? Or are they always -1?

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actually i only pasted few rows of my matrix contains 4200 rows, i think -1 means inhibition and +1 mean activation and 0 means transcription factor does not any effect on the gene but problem is this i don't know how to convert this matrix to a weighted adjacency matrix

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