GlobalAncova.closed-methods: Methods for Function GlobalAncova.closed

In GlobalAncova: Global test for groups of variables via model comparisons

Description

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

Methods

xx = "matrix", test.genes="list", formula.full = "formula", formula.red = "formula", model.dat = "ANY", group = "missing", covars = "missing", test.terms = "missing"

In this method, besides the expression matrix xx and the list of gene groups test.genes, 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", test.genes="list", formula.full = "formula", formula.red = "missing", model.dat = "ANY", group = "missing", covars = "missing", test.terms = "character"

In this method, besides the expression matrix xx and the list of gene groups test.genes, 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", test.genes="list", formula.full = "missing", formula.red = "missing", model.dat = "missing", group = "ANY", covars = "ANY", test.terms = "missing"

Besides the expression matrix xx and the list of gene groups test.genes 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.

GlobalAncova documentation built on Nov. 8, 2020, 8:10 p.m.