Description Usage Arguments Details Value Author(s) See Also
View source: R/termpathsHeadlines.R
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)
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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.) |
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