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Probabilities not adjusted when computing centrality on "netP"

Open ycl6 opened this issue 9 months ago • 0 comments

Based on the current netAnalysis_computeCentrality function, the prob values are adjusted if pval did not meet the thresh, i.e. set to 0 in L206.

https://github.com/sqjin/CellChat/blob/418b660aa896758a6a7858a443c56ffcb522c672/R/analysis.R#L201-L208

However, pval is only provided and stored in net when running the computeCommunProb function. The computeCommunProbPathway function only provides prob and not pval. Therefore methods::slot(object, "netP")$pval is NULL. The probabilities is not adjusted when slot.name = "netP".

ycl6 avatar Sep 28 '23 11:09 ycl6