Added new SEMtree() function for tree-based structure learning methods. Four methods with graph (type= “ST” or “MST”) and data-driven (type = “CAT” or “CPDAG”) algorithms are implemented.
Deprecated activeModule() and corr2graph() functions in favor of new SEMtree() function.
Added new dagitty2graph() function for conversion from a dagitty graph object to an igraph object.
Added new localCI.test() function for local conditional indipendence (CI) test of missing edges from an acyclic graph. This function is a wrapper to the function localTests() from package dagitty.
Added new arguments for SEMace() function: type = c(“parents”, “minimal”, “optimal”) to choose the conditioning set Z of Y over X; effect = c(“all”, “source2sink”, “direct”,) to choose the type of X to Y effect.
Added new argument for SEMdci() function: type = “ace” from ACE function() with fixed type= “parents”, and effect=“direct”
Change mergeGraph() function. Now the function combines groups of graph nodes using hierarchical clustering with prototypes derived from protoclust package or custom membership attribute (e.g., cluster membership derived from function clusterGraph()).
Delete argument seed = c(0.05, 0.5, 0.5) in the function weigthGraph(). Now if group is NOT NULL also node weighting is actived, and node weights correspond to the sign and P-value of the z-test = b/SE(b) from glm(node ~ group).
Various fixed bugs
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
First stable version on CRAN
Update kegg.RData (November, 2021)
Added kegg.pathways.RData (November, 2021)
Added pkgdown website
Various fixed bugs