Design_matrix_and_contrasts.R

# simulate design matrix wti Dx with 3 categories and Sex with 2
# A: Control
# B: Schiz
# C: Other
info = data.frame(Dx = sample(LETTERS[1:3], 100, replace=TRUE),
                  Sex = sample(c('M', 'F'), 100, replace=TRUE))

table(info$Dx)
#> 
#>  A  B  C 
#> 39 29 32
table(info$Sex)
#> 
#>  F  M 
#> 48 52

# Marginal terms
colnames(model.matrix(~ Dx + Sex, info))
#> [1] "(Intercept)" "DxB"         "DxC"         "SexM"
colnames(model.matrix(~ 0+Dx + Sex, info))
#> [1] "DxA"  "DxB"  "DxC"  "SexM"

# Interaction terms
colnames(model.matrix(~ Dx*Sex, info))
#> [1] "(Intercept)" "DxB"         "DxC"         "SexM"        "DxB:SexM"   
#> [6] "DxC:SexM"
colnames(model.matrix(~ 0+Dx*Sex, info))
#> [1] "DxA"      "DxB"      "DxC"      "SexM"     "DxB:SexM" "DxC:SexM"

# Interaction by crossing categories
info$Dx_Sex = with(info, paste(Dx, Sex, sep='.'))
colnames(model.matrix(~Dx_Sex, info))
#> [1] "(Intercept)" "Dx_SexA.M"   "Dx_SexB.F"   "Dx_SexB.M"   "Dx_SexC.F"  
#> [6] "Dx_SexC.M"
colnames(model.matrix(~0+Dx_Sex, info))
#> [1] "Dx_SexA.F" "Dx_SexA.M" "Dx_SexB.F" "Dx_SexB.M" "Dx_SexC.F" "Dx_SexC.M"