Description Usage Arguments Value Cell indices are one-based Note Author(s) References See Also
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.
1 2 3 4 5 6 7 8 9 | 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)
|
filename |
The filename of the CDF file. |
units |
An |
readXY |
If |
readBases |
If |
readIndexpos |
If |
readExpos |
If |
readUnitType |
If |
readUnitDirection |
If |
readUnitNumber |
If |
readUnitAtomNumbers |
If |
readGroupAtomNumbers |
If |
readGroupDirection |
If |
readIndices |
If |
readIsPm |
If |
stratifyBy |
A |
verbose |
An |
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, |
type |
type of the unit. |
direction |
direction of the unit. |
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
.
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.
James Bullard and Kasper Daniel Hansen.
[1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats, June 14, 2005. http://www.affymetrix.com/support/developer/
It is recommended to use readCdfUnits
() instead of this method.
readCdfHeader
() for getting the header of a CDF file.
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