R/motif_data_frame_to_sequence.R

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

#' Convert data frame of motif to the sequence pattern
#'
#' @param motif_data_frame A data frame with two columns including amino acid and index on sequence with fixed length.
#' @param center A character for center of k-mer.
#' @param width A numeric for specific k-mer.
#'
#' @author Dongdong Zhan and Mengsha Tong
#'
#'
#' @return A string for motif pattern
#' @export
#'
#' @examples
#' \dontrun{
#' ftp_url <- "https://github.com/ecnuzdd/PhosMap_datasets/function_demo_data/motif_data_frame_to_sequence.RData"
#' load_data <- load_data_with_ftp(ftp_url, 'RData')
#' writeBin(load_data, "motif_data_frame_to_sequence.RData")
#' load("motif_data_frame_to_sequence.RData")
#'
#' motif_pattern <- motif_data_frame_to_sequence(
#'   motif_coordinate_data_frame,
#'   center, width
#' )
#' head(motif_pattern)
#' }

motif_data_frame_to_sequence <- function(motif_data_frame, center, width){
  motif_pattern <- rep('.', width)
  motif_pattern[ceiling(width/2)] <- center
  motif_data_frame_row <- nrow(motif_data_frame)
  for(i in seq_len(motif_data_frame_row)){
    motif_pattern[motif_data_frame[i,2]] <- motif_data_frame[i,1]
  }
  motif_pattern <- paste(motif_pattern, collapse = '')
  return(motif_pattern)
}