R/get_foreground_df_to_motifs.R

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

#' Get filtered foreground data frame that its aligned sequences with specific motif.
#'
#' @param foreground_sequences_mapped_to_motifs A list that consists of motifs and its corresponding aligned sequences.
#' @param foreground A vector for aligned sequences.
#' @param foreground_df A data frame from the initial foreground data frame.
#'
#' @author Dongdong Zhan and Mengsha Tong
#'
#'
#' @return A data frame that its aligned sequences with specific motif.
#' @export
#'
#' @examples
#' ## The process needs to load data from PhosMap datasets stored into FTP server and perform large computation.
#' ## It may take a few minutes.
#' if(FALSE){
#'     ftp_url <- "https://github.com/ecnuzdd/PhosMap_datasets/function_demo_data/get_foreground_df_to_motifs.RData"
#'     load_data <- load_data_with_ftp(ftp_url, 'RData')
#'     writeBin(load_data, "get_foreground_df_to_motifs.RData")
#'     load("get_foreground_df_to_motifs.RData")
#'
#'     foreground_df_mapped_to_motifs <- get_foreground_df_to_motifs(
#'       foreground_sequences_mapped_to_motifs,
#'       foreground, foreground_df
#'     )
#'    head(foreground_df_mapped_to_motifs)
#' }
#'
#'
#

get_foreground_df_to_motifs <- function(foreground_sequences_mapped_to_motifs, foreground, foreground_df){
  cat('\n', 'Find data frame in foreground that are mapped to specific motif. \n')
  formatted_output_vector <- NULL
  foreground_sequences_mapped_to_motifs_len <- length(foreground_sequences_mapped_to_motifs)
  for(i in seq_len(foreground_sequences_mapped_to_motifs_len)){
    mapped_seq <- foreground_sequences_mapped_to_motifs[[i]]
    formatted_output_vector <- c(formatted_output_vector, mapped_seq)
  }
  index_of_match <- match(formatted_output_vector, foreground)
  foreground_df_mapped_to_motifs <- foreground_df[index_of_match,]
  return(foreground_df_mapped_to_motifs)
}