library(qtl)
set.seed(1000)
version = mqm_version()
cat("R/qtl=",version$RQTL)
cat("R-MQM=",version$RMQM)
cat("MQM=",version$MQM)
testaugmentation <- function(cross, ...){
crossML <- mqmaugment(cross, ...)
crossIMP <- mqmaugment(cross,strategy="impute", ...)
crossDROP <- mqmaugment(cross,strategy="drop", ...)
res1 <- mqmscan(crossML)
res2 <- mqmscan(crossIMP)
res3 <- mqmscan(crossDROP)
plot(res1,res2,res3,lty=c(1,2,3),col=c("black","blue","red"))
legend("topleft",c("MinProb","Imputation","Drop"),lty=c(1,2,3),col=c("black","blue","red"))
list(res1,res2,res3)
}
stabilitytest <- function(cross, ...){
crossML1 <- mqmaugment(cross, minprob=0.5,maxaugind=16,...)
crossML2 <- mqmaugment(cross, minprob=0.05,maxaugind=16,...)
crossML3 <- mqmaugment(cross, minprob=0.005,maxaugind=16,...)
res1 <- mqmscan(crossML1)
res2 <- mqmscan(crossML2)
res3 <- mqmscan(crossML3)
plot(res1,res2,res3,lty=c(1,2,3),col=c("black","blue","red"))
legend("topleft",c("minprob 0.5","minprob 0.05","minprob 0.005"),lty=c(1,2,3),col=c("black","blue","red"))
list(res1,res2,res3)
}
data(multitrait)
multimissing <- simulatemissingdata(multitrait,25)
#r <- stabilitytest(multimissing,verbose=TRUE)
r <- testaugmentation(multimissing)
if(!round(r[[1]][3,3],3)==0.764) stop("Multitrait ML dataaugmentation error")
if(!round(r[[1]][3,3],3)==round(r[[2]][3,3],3)) stop("Multitrait ML compared versus IMP error")
if(!round(r[[3]][3,3],3)==0.844) stop("Multitrait DROP dataaugmentation error")
data(hyper)
r <- testaugmentation(hyper,maxaugind=32,minprob=0.75)
if(!round(r[[1]][3,3],3)==0.568) stop("Hyper ML dataaugmentation error")
if(!round(r[[1]][3,3],3)==round(r[[2]][3,3],3)) stop("Hyper ML compared versus IMP error")
if(!round(r[[3]][3,3],3)==0.252) stop("Hyper DROP dataaugmentation error")
data(listeria)
r <- testaugmentation(listeria)
if(!round(r[[1]][3,3],3)==0.352) stop("Listeria ML dataaugmentation error")
if(!round(r[[1]][3,3],3)==round(r[[2]][3,3],3)) stop("Listeria ML compared versus IMP error")
if(!round(r[[3]][3,3],3)==0.034) stop("Listeria DROP dataaugmentation error")
cat("testaugmentation.R, tests succesfully run!")
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