modelEntry {Envisage} | R Documentation

## Specify a minimum model for step-wise model fitting

### Description

This function allows specification of a minimum model for the step-wise model fitting procedure in the Envisage GUI. This can 'force' terms of interest to always be considered in the model for each gene.

### Usage

      modelEntry(pData, Mentry, useParams, labParams, MEorINT, glm.formula)

### Arguments

`pData` | An object of class `phenoData` containing the phenotypic information for the experiment.
`Mentry` | Object of class `tkentry` containing the model entry field from the Envisage GUI. This is used if the starting model is specified in the GUI.
`useParams` | Character vector containing the variable names to be used in the model fitting procedure.
`labParams` | Output from function `labelParams`, containing the indices of the labelling parameters for the `phenoData` object `pData`.
`MEorINT` | Character string indicating whether to look at main effect terms only ('`ME`') or main effect and interaction terms ('`INT`').
`glm.formula` | Object of class `formula` containing the minimal model for the step-wise model fitting procedure.

### Details

The Envisage package contains methods allowing the use of linear models (LMs) for analysing significantly changing genes in experiments with a variety of sources of variation, be they experimentally controlled variables such as drug treatment or time, or non-controlled sources of confounding variation such as phenotypic or environmental differences. This allows all sources of variation to be considered when analysing for significant differential expression, ensuring resulting genes are biologically relevent to the experimental question.

The function `modelEntry` is used to set up the maximum and minimum models for the Envisage step-wise model fitting procedure. This can be done in one of two ways. If using the command line interface to `envisage`, the model can be explicitly stated in the command line in the form 'X ~ var1 + var2:var3 + etc.'. However, if using the GUI (`widget=TRUE`), users can specify the model in terms of the variable labels (of the form `p1`, `p2`, `p3`, etc. (e.g. `p1+p3+p5:p6`). This function processes these values to give the minimum model for the analysis.

`modelEntry` is an internal function and is not designed to be accessed by users.

### Value

A list is returned with the followig slots:

`startingModel` | An object of class `formula` giving the minimum model for the the step-wise model fitting procedure.
`intPos` | An internal object used to identify the location of interaction terms within the minimum model.

### Author(s)

Sam Robson S.C.Robson@warwick.ac.uk

### References

Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) Envisage: model-based significance analysis of microarray gene expression data, manuscript in preparation

### See Also

For the main Envisage method, see `envisage`.

[Package Envisage version 1.0-2 Index]