R/mea_based_on_background.R

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

#' Motif enrichment based on global background (fasta library from Refseq).
#'
#' @param foreground A vector for aligned sequence of foreground.
#' @param AA_in_protein A vector for the location of S/T/Y in sequence of protein.
#' @param background A vector for aligned sequence of background.
#' @param motifx_pvalue A numeric value for selecting motifs that meets the minimum cutoff.
#'
#' @author Dongdong Zhan and Mengsha Tong
#'
#' @return A list containing motifs and the corresponding sequences
#' @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/mea_based_on_background.RData"
#'     load_data <- load_data_with_ftp(ftp_url, 'RData')
#'     writeBin(load_data, "mea_based_on_background.RData")
#'     load("mea_based_on_background.RData")
#'
#'     motifs_list <- mea_based_on_background(
#'       foreground[1:100],
#'       AA_in_protein[1:100],
#'       background[1:1000],
#'       motifx_pvalue
#'     )
#' }
#'

# foreground <- as.vector(foreground_df$aligned_seq)
# AA_in_protein <- as.vector(foreground_df$AA_in_protein)
mea_based_on_background <- function(foreground, AA_in_protein, background, motifx_pvalue){
  # foreground <- as.vector(foreground)
  # background <- as.vector(background$Aligned_Seq)
  center_vector_candidate <- c('S', 'T', 'Y')
  center_vector_candidate_len <- length(center_vector_candidate)
  center_vector <- NULL
  for(i in seq_len(center_vector_candidate_len)){
    center <- center_vector_candidate[i]
    if(length(grep(center, AA_in_protein)) > 0){
      center_vector <- c(center_vector, center)
    }
  }
  cat('Start executing motifx and find motif pattern. \n')
  cat('Foreground sequences: ', length(foreground), '.\n', sep = '')
  cat('Background sequences: ', length(background), '.\n', sep = '')
  cat('Phosphorylation: [', center_vector, '] exists in foreground.\n', sep = '')
  cat('Motifx pvalue cutoff: ', motifx_pvalue, '.\n', sep = '')
  motifs_list <- get_motifs_list(foreground, background, center_vector, motifx_pvalue)
  cat('Motifx analysis OK! ^_^', '\n')
  print(motifs_list)
  cat('\n')
  return(motifs_list)
}