model.pickgene: Create Model Matrix for Orthogonal Contrasts

In pickgene: Adaptive Gene Picking for Microarray Expression Data Analysis

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"))

Example output

Attaching package: 'pickgene'

The following object is masked from 'package:stats':

    nlminb

  (Intercept)      sex.L    genotype.L genotype.Q
1           1 -0.7071068 -7.071068e-01  0.4082483
2           1 -0.7071068 -7.850462e-17 -0.8164966
3           1 -0.7071068  7.071068e-01  0.4082483
4           1  0.7071068 -7.071068e-01  0.4082483
5           1  0.7071068 -7.850462e-17 -0.8164966
6           1  0.7071068  7.071068e-01  0.4082483
attr(,"assign")
[1] 0 1 2 2
attr(,"contrasts")
attr(,"contrasts")$sex
[1] "contr.poly"

attr(,"contrasts")$genotype
[1] "contr.poly"

pickgene documentation built on Nov. 8, 2020, 6:50 p.m.