R/filterByDefault.R

In anapuce: Tools for Microarray Data Analysis

filterByDefault <-
  function(fileIN,
           flag0,
           m,
           filter.fic = filter.fic,
           filter.var = filter.var,
           sep = sep,
           sep.write = sep.write,
           dec.write = dec.write,
           ...)
  {
    options(warn = -1)
    if (!is.null(filter.fic))
    {
      VarCible <- fileIN[, match(filter.var, colnames(fileIN))]
      aEnlever <- read.table(filter.fic, header = FALSE, sep = sep, ...)
      ValASuppr <-
        unlist(apply(
          aEnlever,
          MARGIN = 1,
          FUN = grep,
          x = as.vector(VarCible)
        ))
      fileIN   <- fileIN[-ValASuppr, ]
    }
    index1 <- numeric()
    for (ii in 1:length(flag0))
    {
      tmpind <- which(fileIN$Flags == flag0[ii])
      cat("Total number of spots with flag",
          flag0[ii],
          ": ",
          length(tmpind),
          "\n")
      if (length(tmpind) != 0) {
        fileflag <- fileIN[fileIN$Flags == flag0[ii], ]
        fileIN  <- fileIN[-tmpind, ]
        write.table(
          fileflag,
          file = paste("ListFlag", flag0[ii], ".txt", sep = ""),
          row.names = FALSE,
          append = TRUE,
          sep = sep.write,
          dec = dec.write
        )
      }
    }
    options(warn = 0)
    fileIN
    # (c) 2007 Institut National de la Recherche Agronomique

  }