#' hmmDI
#'
#' @param fileOutName
#' @param outputPath
#' @param refFragsPATH
#' @param h5PATH
#' @param bintablePath
#' @param bin.size
#'
#' @return
#' @keywords internal
#'
#' @examples
hmmDI<- function (fileOutName, outputPath, refFragsPATH, h5PATH, bintablePath, bin.size){
rFrags<-read.table (refFragsPATH, sep='\t', header=TRUE)
binTab<-read.table (bintablePath, sep='\t', header=FALSE)
rFragsGrange<-GenomicRanges::makeGRangesFromDataFrame(rFrags)
print("star pairparam")
paramFil <- diffHic::pairParam(rFragsGrange)
print("end pairparam")
#h5PATH<<-h5PATH
#paramFil<<-paramFil
#bin.size<<-bin.size
finder <- diffHic::domainDirections(h5PATH, paramFil, width=bin.size, span=10)
print("finded domains")
all.counts <- cbind(SummarizedExperiment::assay(finder, "up"),
SummarizedExperiment::assay(finder, "down"))
DI<-matrix(ncol=2,nrow=length(all.counts[,1]))
DI[,1]<-c(1:length(all.counts[,1]))
colnames(DI)<-c('bin','value')
for (i in 1:length(DI[,1])){
#print (paste0('i:',i,'/',length(DI[,1])))
a<-all.counts[i,1]
b<-all.counts[i,2]
e<-(a+b)/2
DI[i,2]<-((b-a)/abs(b-a))*((((a-e)^2)/e)+ (((b-e)^2)/e) )
}
binNames<-matrix (ncol=1,nrow=length(binTab[,1]))
binNames[,1]<-rep (paste0(binTab[,1],':',binTab[,2],'-',binTab[,3]))
DI[,1]<-binNames[,1]
print("wrote HMM results")
HCRwrite (DI, fileOutName, path=outputPath , quote=FALSE, col.names=TRUE, row.names=TRUE)
return(DI)
}
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