R/get_MHic_data.R

In Skhakmardan/MHiC: MHiC

get_MHic_data<-function(reads_file){
  
  filetype<-grepl("\\.matrix$", reads_file)
  if(!filetype){filetype<-grepl("\\.table$", reads_file)}
  else if(!filetype){
    filetype<-grepl("\\.txt$", reads_file)}
  ##########################################################
  if(filetype){
    reads<-read.matrix(interaction_file, header = FALSE, sep = "\t") 
  }
  else{stop('data must be in MHiC format')}
  
  interactions<-data.frame(reads$V1,reads$V2,reads$V3,reads$V4
                           ,reads$V5)
  
  names(interactions)<-c("chr1", "locus1_start", "chr2", "locus2_start"
                         ,"frequencies")
  return(interactions)
  
}