R/readRS.R

In CL-CHEN-Lab/RepliSeq: Repliseq

#' @title Read Repli-seq assay data (bedgraph format).
#' @description Bedgraphs with a one line header and with similar organization (same length and sorted)
#'
#' @param paths_data list of paths to repliseq fractions files
#' @param fractions list of fractions names
#'
#' @return a dataframe composed of genomic coordinates plus all the specified fractions as for example : chr,start,stop,S1,S2,S3,S4,S5,S6
#' @import magrittr
#' @importFrom dplyr select
#' @importFrom dplyr rename
#' @export


readRS <- function(paths_data,fractions) {
  
  #### Control that path data and fractions are the same length
  if (length(paths_data) != length(fractions)) {
    stop("arguments paths_data and fractions must have the same sizes")
  }
  ### read genomic coordinates from first fraction :
  rs_temp <- read.table(paths_data[1] , header = FALSE , skip=1 , sep="") %>%
    select(V1,V2,V3) %>%
    rename(chr = V1, start = V2, stop = V3)
  ### read other fractions and create the corresponding columns in rs_temp
  for (i in c(1:length(paths_data))) {
    temp_fraction <- fractions[i]
    temp_path <- paths_data[i]
    temp_fraction_df <- read.table(temp_path,header=FALSE,skip=1,sep="")
    rs_temp[temp_fraction] <- temp_fraction_df$V4
  }
  
  return(rs_temp)
  
}