library("gbs2ploidy") ## getting our data ready in R ids<-read.csv("DT_aspen_1Jul16.csv") ## NV17 was dropped = 129 het<-as.matrix(read.table("hetAlleleDepth.txt",header=F)) a<-seq(1,380,2) b<-seq(2,380,2) cov1<-het[,a] cov2<-het[,b] ## drop = 129 to match ids cov1<-cov1[,-129] cov2<-cov2[,-129] ## drop conatminant, FSL 279 = 92 ids and cov ids<-ids[-92,] cov1<-cov1[,-92] cov2<-cov2[,-92] propOut<-estprops(cov1=cov1,cov2=cov2,props=c(0.25, 0.33, 0.5, 0.66, 0.75),mcmc.nchain=3,mcmc.steps=100,mcmc.burnin=10,mcmc.thin=5) H<-apply(is.na(cov1)==FALSE,2,mean) D<-apply(cov1+cov2,2,mean,na.rm=TRUE) out<-estploidy(alphas=propOut,het=H,depth=D,train=FALSE,nclasses=2,ids=ids[,4])