R/splitSeqMotDist.R

In takahirosuzuki1980/InfiniumDiffMetMotR: Motif Overrepresentation analysis for Illumina Methylation Arrays

#' PWM serch for splitted sequence files
#' 
#' PWM serch for all solitted sequence files
#' #Splitted seqs are sequentially read and serched the given PWM
#' 
#' @param filenames list of splitted files
#' @param motif_list PWM list
#' @param min.score The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. "85%") of the highest possible score or as a single number. 
#' 
#' @importFrom Biostrings readDNAStringSet
#' @importFrom pbapply pblapply
#' 
#' @return relative positions of PWM from the probes
#' 
#' @keywords PWM, motif seaech
#' @export

splitSeqMotDist <- function(filenames, motif_list, min.score){
    target_positionsList <- lapply(1:length(motif_list), function(i){ numeric() }) #an object to save result of motif search for all motifs
    names(target_positionsList) <- names(motif_list)
    count <- 1
    for(i in filenames){
        #read the multi-fasta file names one by one
        sto <- paste("    ", i, " is processing......", count, "/", length(filenames), "\n", sep = "")
        cat(sto)
        fasta2 <- readDNAStringSet(i) #read the multi-fasta file as DNAStringSet
        target_posi_subList <- pblapply(motif_list, function(x){ motifDistMultiSeqs(motif = x, fasta2 = fasta2, min.score = min.score) }) #target_posi_subList is a list of lists of identified motif positions in a region for each motif.
        for(j in 1:length(target_posi_subList)){
            target_positionsList[[j]] <- c(target_positionsList[[j]], target_posi_subList[[j]]) #save the result to an List object
        }
        count <- count + 1
        rm(fasta2)
        cat("    Done...\n")
    }
    return(target_positionsList)
}