R/readBetaScoreMatrix.R

In benoukraflab/TFregulomeR: TFregulomeR reveals transcription factors’ context-specific features and functions

readBetaScoreMatrix <- function(betaScore_file_path) {
  if (endsWith(betaScore_file_path, suffix = "NA") != TRUE) {
    con <- tryCatch(
      {
        file(betaScore_file_path, "r")
      },
      warning = function(w) {
        message(paste0("Warning: Please check your id or internect access!"))
        stop()
      },
      error = function(err) {
        message(paste0("Error: Please check your id or internect access"))
      }
    )

    if (!is.null(con)) {
      # beta score vector to store all beta scores
      beta_score <- c()
      n_position <- 0
      while (TRUE) {
        line <- readLines(con, n = 1)
        if (length(line) == 0) {
          break
        }
        line_vector <- unlist(strsplit(as.character(line), split = "\t"))
        n_position <- length(line_vector[-1])
        beta_score <- c(beta_score, line_vector[-1])
      }
      close(con)
      beta_score_matrix <- matrix(
        as.integer(beta_score), ncol = n_position, byrow = TRUE
      )
      beta_score_matrix <- beta_score_matrix[-1, ]
      return(beta_score_matrix)
    } else {
      message(paste0("Beta score matrix for is NULL!"))
      return(NULL)
    }
  } else {
    return(as.matrix(NA))
  }
}