R/MHiC.R

In Skhakmardan/MHiC: MHiC

MHiC<-function(reads_file,Digest_file = NULL,sample_name
               ,tools_name = NULL,res = 1000000 ,cistrans = "all"
               , parallel=FALSE, cores=NULL, removeDiagonal=TRUE){
  #this tools get Hi-C data from different tools
  #function for get different Hi-C structure
  inetractions<-get_Hic_data(reads_file,Digest_file,tools_name)

  #apply user bin size to Hi-C data
  #bin size has to bigger than digest file range
  inetractions<-interaction_res(inetractions,res)

  #apply binomial function for identify significant interaction
  Result<-binomial_function(inetractions,tools_name
                            ,cistrans,parallel
                            ,cores,removeDiagonal)
  #save result
  #his part of tools is  under developing

  return(Result)

}