model.pickgene {pickgene}R Documentation

Create Model Matrix for Orthogonal Contrasts

Description

The function created a model matrix of orthogonal contrasts to be used by pickgene.

Usage

model.pickgene( faclevel, facnames = <<see below>>,
  contrasts.fac = "contr.poly", collapse = "+", show = <<see below>>,
  renorm = 1, modelexpr = <<see below>>, contrasts.list = <<see below>> )

Arguments

faclevel vector with number of levels for each factor
facnames vector of factor names (default = "a","b",...)
contrasts.fac vector of contrast types
collapse "+" for additive model, "*" for full model with interactions
show vector of contrast numbers to show (default is all)
renorm vector to renormalize contrasts (e.g. use sqrt(2) to turn two-condition contrast into fold change)
modelexpr model formula
contrasts.list list of contrasts indexed by index{facnames}

Details

Creates a model matrix data frame with first column having all 1's and other columns having contrasts.

Value

Result of call to model.matrix

Author(s)

Brian Yandell

See Also

model.matrix

Examples

model.pickgene( c(2,3), c("sex","genotype"))

[Package pickgene version 1.0.0 Index]