# sureEps: Epistasis in a SURE model In qtlmt: Tools for Mapping Multiple Complex Traits

## Description

Look for epistasis between existing QTL in a model via model selection.

## Usage

 ```1 2``` ```sureEps(y, x, v, k, direction=c("both","backward","forward"), iter=10000, max.terms=200, steps=1000, tol=1e-12) ```

## Arguments

 `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.

## Value

associated traits, epistatic markers and p-values

## See Also

`surStep`

## Examples

 ``` 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) ```

qtlmt documentation built on May 2, 2019, 2:23 p.m.