Plot.subjects-methods: Methods for Function Plot.subjects
In GlobalAncova: Global test for groups of variables via model comparisons

Description Methods

There are three possible ways of using GlobalAncova, use methods ? GlobalAncova for getting more information. Also Plot.subjects can be invoked with these three alternatives.

xx = "matrix", formula.full = "formula", formula.red = "formula", model.dat = "ANY", group = "missing", covars = "missing", test.terms = "missing": In this method, besides the expression matrix xx, model formulas for the full and reduced model and a data frame model.dat specifying corresponding model terms have to be given. Terms that are included in the full but not in the reduced model are those whose association with differential expression will be tested. The arguments group, covars and test.terms are '"missing"' since they are not needed for this method.
xx = "matrix", formula.full = "formula", formula.red = "missing", model.dat = "ANY", group = "missing", covars = "missing", test.terms = "character": In this method, besides the expression matrix xx, a model formula for the full model and a data frame model.dat specifying corresponding model terms are required. The character argument test.terms names the terms of interest whose association with differential expression will be tested. The arguments formula.red, group and covars are '"missing"' since they are not needed for this method.
xx = "matrix", formula.full = "missing", formula.red = "missing", model.dat = "missing", group = "ANY", covars = "ANY", test.terms = "missing": Besides the expression matrix xx a clinical variable group is required. Covariate adjustment is possible via the argument covars but more complex models have to be specified with the methods described above. This method emulates the function call in the first version of the package. The arguments formula.full, formula.red, model.dat and test.terms are '"missing"' since they are not needed for this method.