readCdf {affxparser} | R Documentation

## Parsing a CDF file using Affymetrix Fusion SDK

### Description

Parsing a CDF file using Affymetrix Fusion SDK. This function parses a CDF file using the Affymetrix Fusion SDK. This function will most likely be replaced by the more general `readCdfUnits()` function.

### Usage

     readCdf(filename, units=NULL,
             readXY=TRUE, readBases=TRUE,
             readIndexpos=TRUE, readAtoms=TRUE,
             readUnitType=TRUE, readUnitDirection=TRUE,
             readUnitNumber=TRUE, readUnitAtomNumbers=TRUE,
             readGroupAtomNumbers=TRUE, readGroupDirection=TRUE,
             readIndices=FALSE, readIsPm=FALSE,
             stratifyBy=c("nothing", "pmmm", "pm", "mm"),
             verbose=0)

### Arguments

`filename` | The filename of the CDF file.
`units` | An `integer` `vector` of unit indices specifying which units to be read. If `NULL`, all units are read.
`readXY` | If `TRUE`, cell row and column (x,y) coordinates are retrieved, otherwise not.
`readBases` | If `TRUE`, cell P and T bases are retrieved, otherwise not.
`readIndexpos` | If `TRUE`, cell indexpos are retrieved, otherwise not.
`readExpos` | If `TRUE`, cell "expos" values are retrieved, otherwise not.
`readUnitType` | If `TRUE`, unit types are retrieved, otherwise not.
`readUnitDirection` | If `TRUE`, unit directions are retrieved, otherwise not.
`readUnitNumber` | If `TRUE`, unit numbers are retrieved, otherwise not.
`readUnitAtomNumbers` | If `TRUE`, unit atom numbers are retrieved, otherwise not.
`readGroupAtomNumbers` | If `TRUE`, group atom numbers are retrieved, otherwise not.
`readGroupDirection` | If `TRUE`, group directions are retrieved, otherwise not.
`readIndices` | If `TRUE`, cell indices calculated from the row and column (x,y) coordinates are retrieved, otherwise not. Note that these indices are one-based.
`readIsPm` | If `TRUE`, cell flags indicating whether the cell is a perfect-match (PM) probe or not are retrieved, otherwise not.
`stratifyBy` | A `character` string specifying which and how elements in group fields are returned. If `"nothing"`, elements are returned as is, i.e. as `vector`s. If `"pm"`/`"mm"`, only elements corresponding to perfect-match (PM) / mismatch (MM) probes are returned (as `vector`s). If `"pmmm"`, elements are returned as a matrix where the first row holds elements corresponding to PM probes and the second corresponding to MM probes. Note that in this case, it is assumed that there are equal number of PMs and MMs; if not, an error is generated. Moreover, the PMs and MMs may not even be paired, i.e. there is no guarantee that the two elements in a column corresponds to a PM-MM pair.
`verbose` | An `integer` specifying the verbose level. If 0, the file is parsed quietly. The higher numbers, the more details.

### Value

A list with one component for each unit. Every component is again a list with three components

`groups` | This is again a list with one component for each group (also called block). The information on each group is a list with 5 components, `x`, `y`, `pbase`, `tbase`, `expos`.
`type` | type of the unit.
`direction` | direction of the unit.

### Cell indices are one-based

Note that in affxparser all cell indices are by convention one-based, which is more convenient to work with in R. For more details on one-based indices, see `2. Cell coordinates and cell indices`.

### Note

This version of the function does not return information on the QC probes. This will be added in a (near) future release. In addition we expect the header to be part of the returned object.

So expect changes to the structure of the value of the function in next release. Please contact the developers for details.

### Author(s)

James Bullard and Kasper Daniel Hansen.

### References

[1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats, June 14, 2005. http://www.affymetrix.com/support/developer/

### See Also

It is recommended to use `readCdfUnits`() instead of this method. `readCdfHeader`() for getting the header of a CDF file.

[Package affxparser version 1.56.0 Index]