Nothing
IBDcheck<-function(dat,filterparams=filter.control(),simparams=sim.control())
{
call<-match.call() # store function call for later use
# step0: error checking.
if(!is.IBD(dat)) {
stop("Input must be an object of class IBD")
}
# Check that user's list of relationships for gene drops makes sense
if(simparams$simulate) {
# Then we will be doing gene drops
allrships<-c("MZtwins","unrelated","parent-offspring","full-sibs","half-sibs","cousins","user")
simparams$rships<-match.arg(simparams$rships,allrships,several.ok=TRUE)
names(simparams$nsim)<-simparams$rships
# above will cause function to exit with an error if it finds a
# relationship in simparams$rships with no match in allrships.
}
# Finished error checking
# apply QC filters to SNPs and subjects, if necessary
if(filterparams$filter) {
dat <- snpfilter(dat,filterparams)
}
cdlibs <- cdlIBS(dat)
# Save cldibs for future calls
dat$snp.support<-add.cdlIBS(dat$snp.support,cdlibs)
if(is.null(dat$ibd.study) || filterparams$filter) {
# need to compute or recompute ibd coefficients for study data
dat$ibd.study=IBDest.study(dat$snp.data, cdlibs)
}
if(simparams$simulate){
snpmats=simIBD(dat,simparams)
rships.ab<-c("ur","mz","po","fs","hs","co","user") #abbreviated names
ibd.objs<-paste("ibd",rships.ab,sep=".")
# loop over relationships requested by the user
for(i in 1:length(ibd.objs)) {
ibd.tem<-IBDest.sim(snpmats[[rships.ab[i]]],cdlibs)
dat[[ibd.objs[i]]]<-rbind(dat[[ibd.objs[i]]],ibd.tem) # add to any existing simulated pairs
}
simparams$LDfiles<-snpmats$LDfiles
}
# Return an object of class IBD
dat$filterparams<-filterparams
dat$simparams<-simparams
dat$call<-call
return(dat)
# Return an object of class IBD, created by the IBD constructor function.
#return(IBD(dat$snp.data,dat$snp.support,dat$subject.support,
# ibd.study,ibd.ur,ibd.mz,ibd.po,ibd.fs,ibd.hs,ibd.co,ibd.user,
# filterparams,simparams,call))
}
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