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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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Incorporating a network model into an MLM #137

Open rbutleriii opened 1 month ago

rbutleriii commented 1 month ago

Hi,

Wondering if it it is possible to incorporate more complex prior information into the mlm or one of the other available models. I have gene data that is stored in a set of igraphs for each pathway I am analyzing, with edge values connecting genes and node values that represent scores for the genes themselves.

It doesn't seem like the network data.frame can have columns for Pathway, source_gene, target_gene, mor. Although, a workaround would be if the framework could accept multiple frames of prior information. One network would be the node scores, and the other would be a simplified neighbor score for each node, similar to NGSEA generating a mean of the absolute value of the gene-based scores of its network neighbors, or alternately some other metric of network centrality.

PauBadiaM commented 3 days ago

Hi @rbutleriii,

Apologies for the delayed response. You can infer pathway activity by treating pathways as sources and each edge of the network as a node with a specific mode as the target. Alternatively, you could take an iterative approach: start by computing activities from the "leaf" sources, and then iteratively calculate activities until you reach the "root." We’ve implemented a similar approach to this in a recent preprint: https://doi.org/10.1101/2024.07.15.603538 Hope this is helpful!