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Probabilities not adjusted when computing centrality on "netP"
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"
.