Description Usage Arguments Value See Also Examples
Look for epistasis between existing QTL in a model via model selection.
1 2 |
y |
a n by p matrix, whose columns are dependent variables. |
x |
a n by m matrix, whose columns are predictor variables |
v |
a list; v[[j]] indicates which x's in the model for y[,j], between which possible epistasis is looked for. |
k |
penalty, 0 if missing or <0. |
direction |
forward selection, backward elimination or stepwise. |
iter |
maximum number of iterations in a numerical process to estimate model parameters. |
max.terms |
maximum number of terms in the final model. |
steps |
maximum number of search steps. |
tol |
convergence tolerance. |
associated traits, epistatic markers and p-values
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | data(etrait)
x<- as.matrix(mdat-1/2)
y<- as.matrix(traits)[,1:3]
v<- list()
upper<- list()
for(k in 1:ncol(y)){
v[[k]]<- numeric(0)
upper[[k]]<- 1:ncol(x)
}
## Not run:
o<- surStep(y, x, v=v, upper=upper, k=19, direction="both",
iter=250, max.terms=250, steps=2000, tol=1e-12)
neps<- 6 # suppose there are 6 possible epistatic effects
oeps<- sureEps(y, x, o$v, k=qchisq(1-0.05/neps,1), direction="backward",
iter=250, max.terms=200, steps=1000, tol=1e-12)
## End(Not run)
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