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varnivey / ipanda

insilico Pathway Activation Network Decomposition Analysis (iPANDA) package. Owned by Insilico Medicine Inc. iPANDA is a pathway analysis method that aids interpretation of large-scale gene expression data. The method introduced here includes coexpression analysis and gene importance estimation to robustly identify relevant pathways and biomarkers for patient stratification.
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Question on WipT Calculation and pathway_akk #2

Open dcgemperline opened 7 years ago

dcgemperline commented 7 years ago

Hello,

I have a questinon on how the calculation for WipT is implemented. The Nip computation seems relatively straightforward, but how is Njp defined? It is unclear in your manuscript what Njp refers to. I've done some cursory searching through your code; however I cannot find how WipT is calculated? Additionally in your code, what do the abbreviations ARR and CNR stand for? Thank you!

David

varnivey commented 7 years ago

Hi David!

Thank you for your interest in our work. Excuse me for the delayed response. I was quite busy last week. So calculation of Njp is straightforward as well. Njp refers to maximum number of walks possible through a single gene unit in a pathway. Gene unit may be represented either by an individual gene or by a gene module. Prior to the calculation of the walks through the graph, the actual graph is transformed in a way that all the genes included into a gene module are merged into a single node.

Then WipT for each gene unit is calculated according to the formula 4 from the Methods section of the manuscript.

ARR and CNR in the code refer to Aip and fci in the manuscript respectively.

We have a large number of already preprocessed pathway databases including NCI, KEGG, Reactome, Biokarta and so on. As they are considered as a part of company's IP, I can not share them directly, but we can collaborate on your project if such collaboration may be of interest for your team.

Regards, Ivan

2017-02-17 20:06 GMT+03:00 David notifications@github.com:

Hello,

I have a questinon on how the calculation for WipT is implemented. The Nip computation seems relatively straightforward, but how is Njp defined? It is unclear in your manuscript what Njp refers to. I've done some cursory searching through your code; however I cannot find how WipT is calculated? Additionally in your code, what do the abbreviations ARR AND CNR stand for? Thank you!

David

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jgarces02 commented 5 years ago

Hi @varnivey,

I understand databases you generated have a kind of copyright but is there any script or easy way to do this calculation?

Thanks a lot!