GlobalAncova-methods: Methods for Function GlobalAncova

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

Description

There are three possible ways of using GlobalAncova. The general way is to define formulas for the full and reduced model, respectively, where the formula terms correspond to variables in model.dat. An alternative is to specify the full model and the name of the model terms that shall be tested regarding differential expression. In order to make this layout compatible with the function call in the first version of the package there is also a method where simply a group variable (and possibly covariate information) has to be given. This is maybe the easiest usage in cases where no 'special' effects like e.g. interactions are of interest.

Methods

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 basic idea behind this method is that one can select single terms, possibly from the list of terms provided by previous GlobalAncova output, and test them without having to specify each time a model formula for the reduced model. 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.

hummelma/GlobalAncova documentation built on Feb. 4, 2021, 8:25 a.m.