pickgene (version 1.44.0)

model.pickgene: 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

Value

Result of call to model.matrix

Details

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

See Also

model.matrix

Examples

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