R/chain.import.R

In BayHap: Bayesian analysis of haplotype association using Markov Chain Monte Carlo

`chain.import` <-
function (x, type = "ASCII",keep.rares.chain=FALSE) 
{    
    
     
     if (class(x)=="reg"){    
         a<-print.reg(list(x,TRUE))
         x[[length(x)]]<-as.data.frame(x[[length(x)]])
         b<-a[[2]]$Haplotypes
         names(x[[length(x)]])<-c(a[[1]]$Haplotypes[-length(a[[1]]$Haplotypes)],paste("reg.",b,sep=""))
     }

     if (class(x)=="freq"){
         a<-print.freq(x)
         x[[length(x)]]<-as.data.frame(x[[length(x)]][,1:nrow(a)])
         names(x[[length(x)]])<-a$Haplotypes
     }
     
     if ((keep.rares.chain==FALSE)&&(class(x)=="reg")){
         i<-1
         col.ok<-NULL
         for (i in 1:ncol(x[[length(x)]])){ 
              col.ok<-c(col.ok,!("reg.Rares"%in%strsplit(names(x[[length(x)]]),split=":",fixed=TRUE)[[i]]))       
         }
         x[[length(x)]]<-x[[length(x)]][,col.ok]
     }
     
     x[[length(x)]]<-as.matrix(x[[length(x)]])
     link <- NULL
     link <- x[[length(x)]]   
     return(is.matrix(link) && boa.chain.add(link, "mcmc"))
}