Documentation for sim.cross with 4way seems incomplete

[timflutre]

Here is what I get with the code from CRAN:

> library(qtl)
> map <- sim.map(include.x=FALSE, sex.sp=TRUE)
> model <- rbind(c(1,45,1), c(5,20,-0.5))
> cross <- sim.cross(map, model, n.ind=100, type="4way")
Error in sim.cross.4way(map, model, n.ind, error.prob, missing.prob, partial.missing.prob,  :
  Model must be a matrix with 5 columns (chr, pos and effects).

Should there really be 5 columns, or should the "5" in the code be replaced by "3" to be consistent with the manual (obtained via ?sim.cross)?

[kbroman]

For a backcross, you could use

model <- rbind(c(1,45,1), c(5,20,-0.5))

But for an intercross, you'd need to provide both additive and dominance effects

model <- rbind(c(1,45,1,0), c(5,20,-0.5,0))

And for a 4-way cross, you need to provide 3 effects, since there are four possible genotypes

model <- rbind(c(1,45,1,1,1), c(5,20,-0.5,-0.5,-0.5))

Under "Details", it says:

"For a four-way cross, the effect of a QTL is a set of three numbers, (a,b,c), where, in the case of one QTL, the mean phenotype, conditional on the QTL genotyping being AC, BC, AD or BD, is a, b,c or 0, respectively."

karl

On May 14, 2014, at 8:47 AM, Timothée Flutre notifications@github.com wrote:

Here is what I get with the code from CRAN:

library(qtl) map <- sim.map(include.x=FALSE, sex.sp=TRUE) model <- rbind(c(1,45,1), c(5,20,-0.5)) cross <- sim.cross(map, model, n.ind=100, type="4way") Error in sim.cross.4way(map, model, n.ind, error.prob, missing.prob, partial.missing.prob, : Model must be a matrix with 5 columns (chr, pos and effects).

Should there really be 5 columns, or should the "5" in the code be replaced by "3" to be consistent with the manual (obtained via ?sim.cross)?

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[timflutre]

Thanks, sorry!