R: Function to immitate Affymetrix' gtype\_cel\_to\_pq software

gtypeCelToPQ {aroma.apd} | R Documentation

## Function to immitate Affymetrix' gtype\_cel\_to\_pq software

### Description

Function to immitate Affymetrix' gtype\_cel\_to\_pq software.

### Usage

    ## Default S3 method:
    gtypeCelToPQ(filename, units=NULL, ..., cdf=NULL, nbrOfQuartets=NULL, verbose=FALSE)

### Arguments

`filename` | The name of a CEL file.
`units` | Indices of CDF units to be returned.
`...` | Arguments passed to `readCelUnits`.
`cdf` | A CDF `list` structure, the pathname of the CDF file, or `NULL`. If `NULL`, the CDF file corresponding to the chip type of the CEL file is searched for using `findCdf`.
`nbrOfQuartets` | The number of probe quartets in the returned `matrix`.
`verbose` | See `Verbose`.

### Value

Returns an NxK `matrix` where N is the number of probesets (SNPs) and K=4*Q where Q is the number of probe quartets (PMA,MMA,PMB,MMB). The rownames corresponds to the probeset names.

### Author(s)

Henrik Bengtsson

### References

[1] Affymetrix, Genotyping Probe Set Structure, Developers' Network, White paper, 2005-2015.

### See Also

`gtypeCelToPQ`(). `applyCdfGroups`.

### Examples

    # Scan for CEL files
    files <- list.files(pattern="[.](cel|CEL)$")

    # Convert each to RAW file
    for (file in files) {
      rawFile <- gsub("[.][^.]*$", ".raw", file)
      file.remove(rawFile)
      cel <- gtypeCelToPQ(file, verbose=TRUE)
      write.table(file=rawFile, cel, sep="\t", quote=FALSE)
    }

[Package aroma.apd version 0.6.0 Index]