[R] two cols in a data frame are the same factor

[Andres Legarra]

Dear all,
 I have a data set (QTL detection) where I have two cols of factors in
 the data frame that correspond logically (in my model) to the same
 factor. In fact these are haplotype classes.
 Another real-life example would be family gas consumption as a
 function of car company (e.g. Ford, GM, and Honda) (assuming 2 cars by
 family).

 An artificial example follows:
 set.seed(1234)
 L3 <- LETTERS[1:3]
 (d <- data.frame( y=rnorm(10), fac=sample(L3, 10,
 repl=TRUE),fac1=sample(L3,10,repl=T)))

  lm(y ~ fac+fac1,data=d)

 and I get:

 Coefficients:
 (Intercept)         facB         facC        fac1B        fac1C
     0.3612      -0.9359      -0.2004      -2.1376      -0.5438

 However, to respect my model, I need to constrain effects in fac and
 fac1 to be the same, i.e. facB=fac1B and facC=fac1C. There are
 logically just 4 unknowns (average,A,B,C).
 With continuous covariates one might do y ~ I(cov1+cov2), but this is
 not the case.

 Is there any trick to do that?
 Thanks,

 Andres Legarra
 INRA-SAGA
 Toulouse, France