Major release with significant changes:
Added new arguments for SEMdag() function: LO = “TO” or “TD” for knowledge-based topological order or data-driven top-down order, and penalty = TRUE or FALSE, separate penalty factors can be applied to each coefficient
Deprecated extendGraph() in favor of new resizeGraph() function, that re-sized graph, removing edges or adding edges/nodes if they are present or absent in a given reference network
Change modelSerch(), interactive procedure is out, and now a three step procedure is implemented for search strategies with new SEMdag() and resizeGraph functions
Change SEMgsa() deleting D,A,E p-values with more performing activation and inhibition pvalues
Added argument MCX2= TRUE or FALSE for Shipley.test() function, a Monte Carlo P-value of the combined C test
Added new SEMdci() function for differentially connected genes inference
Change properties(), now extracted components are order by component sizes
Change argument q = q-quantile with q = 1-top/vcount(graph) in activeModule() function, now the induced graph for the “rwr” and “hdi” algorithms is defined by the top-n ranking nodes.
Various fixed bugs…
orientEdges functiongraph2dagitty functionpbapply package