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ma-compbio / Phylo-HMRF

MIT License
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How do I know the correspondence between numbers and states? #3

Open Xie-Bo-2018 opened 5 years ago

Xie-Bo-2018 commented 5 years ago

Hi， How can I relate the number to the state, for example, 1-NC−pan_low, 2-NC−pyg_high, how can I know the correspondence?

Thanks!

yangymargaret commented 5 years ago

Hi xie-pgg @xie-pgg, Thank you for your question. The correspondence between the number and a specific pattern is interpreted by observing the feature distributions of the compared species in each state after the states have been estimated. For example, we estimated 10 states. For samples estimated to be state 1, we find the bonobo has low feature values while the other species have higher values, we interpret state 1 as NC-pan_low (non-conserved, bonobo-specific low). The other states are interpreted in a similar way. For the present method, we interpret the pattern of each state mainly by manual inspection and did not automatically generate the interpretation of each state. Please let me know if you have any other questions. Thanks!