readCdfDataFrame: Reads units (probesets) from an Affymetrix CDF file
In affxparser: Affymetrix File Parsing SDK

Description Usage Arguments Value Author(s) References See Also Examples

Reads units (probesets) from an Affymetrix CDF file. Gets all or a subset of units (probesets).

1 2	readCdfDataFrame(filename, units=NULL, groups=NULL, cells=NULL, fields=NULL, drop=TRUE, verbose=0)

`filename`	The filename of the CDF file.
`units`	An `integer` `vector` of unit indices specifying which units to be read. If `NULL`, all are read.
`groups`	An `integer` `vector` of group indices specifying which groups to be read. If `NULL`, all are read.
`cells`	An `integer` `vector` of cell indices specifying which cells to be read. If `NULL`, all are read.
`fields`	A `character` `vector` specifying what fields to read. If `NULL`, all unit, group and cell fields are returned.
`drop`	If `TRUE` and only one field is read, then a `vector` (rather than a single-column `data.frame`) is returned.
`verbose`	An `integer` specifying the verbose level. If 0, the file is parsed quietly. The higher numbers, the more details.

An NxK data.frame or a vector of length N.

Henrik Bengtsson

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

For retrieving the CDF as a list structure, see readCdfUnits.

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if (require("AffymetrixDataTestFiles")) {            # START #
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# Find any CDF file
cdfFile <- findCdf()

units <- 101:120
fields <- c("unit", "unitName", "group", "groupName", "cell")
df <- readCdfDataFrame(cdfFile, units=units, fields=fields)
stopifnot(identical(sort(unique(df$unit)), units))

fields <- c("unit", "unitName", "unitType")
fields <- c(fields, "group", "groupName")
fields <- c(fields, "x", "y", "cell", "pbase", "tbase")
df <- readCdfDataFrame(cdfFile, units=units, fields=fields)
stopifnot(identical(sort(unique(df$unit)), units))


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}                                                     # STOP #
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