Plot.genes-methods {GlobalAncova} | R Documentation

## Methods for Function Plot.genes

### Description

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

### 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 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.

[Package GlobalAncova version 4.6.0 Index]