Network permutations

Shivangi Agarwal

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Apr 9, 2018, 10:35:03 PM4/9/18

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Hi

I am not clear regarding why hotnet2 is using network permutations of the real network (-np). Can you please tell?.

matthe...@brown.edu

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Apr 9, 2018, 10:43:22 PM4/9/18

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Hi Shivangi,

The network permutations help specify the delta parameter that helps determine the hot subnetworks. Please see step 3 of the online methods in the HotNet2 paper and Section 1.4.2 of the supplement to the HotNet2 paper.

Best,

Matt

Shivangi Agarwal

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Apr 14, 2018, 3:42:54 AM4/14/18

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As suggested, I have gone through the supplementary file. It is written there that "delta is calculated to ensure that the large subnetworks found in the actual network and not in the real network". But what is the formula for calculating delta and also how it is ensuring for the same?. I am not clear. Please explain.

matthe...@brown.edu

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Apr 15, 2018, 6:23:23 PM4/15/18

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Hi Shivangi,

The choice of the delta parameter determines the sizes of the HotNet2 subnetworks. I was unable to find the text that you quoted: "delta is calculated to ensure that the large subnetworks found in the actual network and not in the real network".

For each permuted network, HotNet2 finds the smallest delta such that the size of the largest HotNet2 subnetwork is less than or equal to L_max. HotNet2 chooses delta for the observed network as the median of these delta values across permuted networks. By default, HotNet2 repeats this procedure for L_max = 5, 10, 15, 20.

Please see Section 1.4.3 of the supplement to the HotNet2 paper for more details.