modelEntry {Envisage} | R Documentation |
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.
modelEntry(pData, Mentry, useParams, labParams, MEorINT, glm.formula)
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. |
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.
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. |
Sam Robson S.C.Robson@warwick.ac.uk
Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) Envisage: model-based significance analysis of microarray gene expression data, manuscript in preparation
For the main Envisage method, see
envisage
.