R: Generates an APD file from an Affymetrix CEL file

celToApd {aroma.apd} | R Documentation

## Generates an APD file from an Affymetrix CEL file

### Description

Generates an APD file from an Affymetrix CEL file.

### Usage

    ## Default S3 method:
    celToApd(filename, apdFile=NULL, mapType="asChipType", writeMap=NULL, ..., verbose=FALSE)

### Arguments

`filename` | The pathname of the CEL file.
`apdFile` | An optional pathname of the APD file, otherwise it will be the same as the CEL file with extension replaced with 'apd'.
`mapType` | The type of read map for the generated APD file. If `NULL`, no remapping of the cell indices is done. If `"asChipType"`, the map type is the same as the chip type of the CEL file. If any other `character` string, it sets the map type to that string. Note that there must be a APD map file with this type that can be found by `findApdMap`().
`writeMap` | An optional write map `integer` `vector` used to remap the cell indices for optimal reading speed. If `NULL`, the write map may be obtained from the read map file specified by the `mapType` argument.
`...` | Additional arguments passed to `writeApd`().
`verbose` | A `Verbose` object.

### Value

Returns (invisibly) the pathname of the written APD file.

### Author(s)

Henrik Bengtsson

### See Also

To create an APD map file from a CDF file, see `cdfToApdMap`(). To read an APD file, see `readApd`(). To read an APD map file, see `readApdMap`().

### Examples

    library("R.utils")  ## Arguments

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # 1. Scan for existing CEL files
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # a) Scan for CEL files
    files <- list.files(pattern="[.](cel|CEL)$")
    files <- files[!file.info(files)$isdir]
    if (length(files) > 0 && require("affxparser")) {
      cat("Create an optimal read map for CEL file:", files[1], "\n")
      cdffile <- findCdf(readCelHeader(files[1])$chiptype)
      res <- cdfToApdMap(cdffile)

      cat("Converting CEL file to APD file:", files[1], "\n")
      apdfile <- celToApd(files[1])
      cat("Created APD file:", apdfile, "\n")
      file.remove(apdfile)

      cat("Converting CEL file to APD file with an optimized read map:", files[1], "\n")
      apdfile <- celToApd(files[1], mapType=res$mapType)
      cat("Created APD file:", apdfile, "\n")

      writeMap <- invertMap(res$readMap)
      for (file in files[-1]) {
        cat("Converting CEL file to APD file with an optimized read map:", file, "\n")
        apdfile <- celToApd(file, mapType=res$mapType, writeMap=writeMap)
        cat("Created APD file:", apdfile, "\n")
      }
    } # if (length(files) > 0)

[Package aroma.apd version 0.6.0 Index]