R/get_Hic_data.R

In Skhakmardan/MHiC: MHiC

get_Hic_data<-function(reads_file,Digest_file= NULL,tools_name){
  
  #
  if(is.null(tools_name)){
    
    interactions<-get_MHic_data(reads_file)
  }
  ##########################################################
  
  if(tools_name == 'HiC_PRO'|tools_name == 'HIC_PRO' |tools_name == 'hic_pro' |tools_name == 'Hic_Pro'){
    
    if(is.null(Digest_file)){
      
      interactions<-get_MHic_data(reads_file)
    }
    else{
      interactions<-get_Hic_pro(reads_file,Digest_file)
      }
    
  }
  ##########################################################
  
  else if(tools_name == 'HiCUP' | tools_name == 'HICUP'|tools_name == 'hicup'){
    
    if(is.null(Digest_file)){
      
      interactions<-get_MHic_data(reads_file)
    }
    else{
      interactions<-get_HiCUP(reads_file,Digest_file)}
  }
  ##########################################################
  
  else if(tools_name == 'HOMER' | tools_name == 'homer'){
    
    interactions<-get_HOMER(reads_file)
  }
  ##########################################################
  
  return(interactions)
}