Entering edit mode
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
What are the possible states for InteractionType? -1, 0 and 1? Or are they always -1?
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