R/readPathwayToSignature.R

In zgyaru/testSctpa: A portable toolkit for pathway activity score calculation

#' Reads in a list of signature input files.
#' @param filenames a list of paths to signature input files
#' @return List of Signature Objects
readSignaturesInput <- function(filenames) {
  
  # Create a dictionary to easily compute signature sign
  keys <- c("none" = 1.0,  "up" = 1.0, "plus" = 1.0, "down" = -1.0,
            "dn" = -1.0, "minus" = -1.0, "mius" = -1.0)
  
  
  # Create a list to store all signatures
  sig_data <- list()
  
  for (filename in filenames) {
    message("Loading data from ", filename, " ...")
    
    if (!file.exists(filename)) {
      stop(paste0("Cannot find file: ", filename))
    }
    
    conn <- file(filename, open = "r")
    lines <- readLines(conn, warn = FALSE)
    close(conn)
    
    lines <- trimws(lines)
    lines <- strsplit(lines, "\t")
    
    # Remove invalid lines
    lines <- lines[vapply(lines,
                          function(x) length(x) >= 3, TRUE)]
    
    for (line in lines) {
      
      genes <- c()
      values <- c()
      
      sig <- line[1]
      description <- line[2]
      gene_fields <- line[3:length(line)]
      
      sig_parts <- unlist(strsplit(sig, "_"))
      key <- tolower(sig_parts[[length(sig_parts)]])
      
      if (is.element(key, names(keys))) {
        sig_name <- paste(sig_parts[1:length(sig_parts) - 1],
                          collapse = "_")
      } else {
        key <- "none"
        sig_name <- sig
      }
      
      
      for (k in gene_fields) {
        elem <- strsplit(k, ",")[[1]]
        
        if (length(elem) > 1) { # if the format is gene,value
          gene <- elem[1]
          value <- as.numeric(elem[2])
        } else {
          gene <- elem[1]
          value <- keys[key]
        }
        
        genes <- c(genes, gene)
        values <- c(values, value)
      }
      
      names(values) <- genes
      
      ## sig_name: name of pathway
      ## sig_data[[sig_name]]: a Signature object
      ## sig_data[[sig_name]]$sigDict: genes in signature 
      ##                    a vector, name is gene, value is rep(1)
      
      if (sig_name %in% names(sig_data)) {
        existingSig <- sig_data[[sig_name]]
        existingSig@sigDict[toupper(names(values))] <- values
        sig_data[[sig_name]] <- existingSig
      } else {
        #print(names(values))
        #print(sig_name)
        #print(filenames)
        newSig <- Signature(sigDict = values, 
                            name = sig_name,
                            source = filename, 
                            metaData = description)
        sig_data[[sig_name]] <- newSig
      }
    }
    
  }
  
  return (sig_data)
}
Signature <- setClass("Signature",
                      slots = c(
                        sigDict = "vector",
                        name = "character",
                        source = "character",
                        metaData = "character"
                      ),
                      prototype = list(
                        metaData = ""
                      ))