readCdf: 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 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

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.

References