termpathsHeadlines: Calculates headlines for each path from root to GO detail...
In CLippmann/ORA: Overrepresentation Analysis

Description Usage Arguments Details Value Author(s) See Also

Calculates headlines for each path from root to GO detail terms. Headlines represent most important nodes in these paths.

1	termpathsHeadlines(AdjMatrix, GOtermNr, Importance, OntologyNr = 1)

`AdjMatrix`	Numeric; Adjacency matrix of GO terms. AdjMatrix[i,j] == 1 if there exists an edge in GO-DAG from node i to node j (i is parent of j).
`GOtermNr`	Numeric; Vector of all GO term numbers that are in the considered DAG. Corresponding to rows and columns of AdjMatrix.
`Importance`	Numeric; Values between 0 and 100. Vector of importance values (= rowwise minimum of (partial shannon) information value and certainty) for GO terms.
`OntologyNr`	Numeric; Default = 1 To select the ontology in which the GOtermNrs are. One of: 1 for biological process, 2 for molecular function or 4 for cellular component.

PLEASE NOTE: All given GO terms have to be in the specified ontology and all ancestors from GO terms to ontology root (including the root-term itself) must be included in the given vector of GO terms.

`Headlines`	Numeric; Vector of GO term numbers that are headlines, the GO term numbers with maximum importance value for each path from detail to GOroot.
`AllTaxonomies`	List of paths from GOroot to all details given by AdjMatrix in form of GO term numbers vectors. (E.g. AllTaxonomies[[1]]==c(8150, 44699, 44763, 22402, 51231, 22) is a path from BP-root "GO:0008150" to detail "GO:0000022"via nodes 44699, 44763, 22402 and 51231 in BP gene ontology.)
`MaxImportanceInd`	Vector of indices which indicate the position of the highest value of importance in the paths in AllTaxonomies. (E.g. MaxImportanceInd==c(2,4,5) then AllTaxonomies[[1]][2] would be the GO term with the highest importance value (i.e. headline) in the first path, AllTaxonomies[[2]][4] the one in the second path and AllTaxonomies[[3]][5] the one in the third path.)