readCdf: Parsing a CDF file using Affymetrix Fusion SDK

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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.
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 vectors. If "pm"/"mm", only elements corresponding to perfect-match (PM) / mismatch (MM) probes are returned (as vectors). 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.

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.