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 = letters[seq(length(faclevel))],
               contrasts.fac = "contr.poly", collapse = "+", show =
               NULL, renorm = 1, modelexpr = formula(paste("~",
               paste(facnames, collapse = collapse))),
               contrasts.list = contr.list)

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 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 1.18.0 Index]