aroma.affymetrix (version 2.2.0)

readCdfDataFrame: Reads units (probesets) from an Affymetrix CDF file

Description

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

Usage

readCdfDataFrame(filename, units=NULL, groups=NULL, cells=NULL, fields=NULL, drop=TRUE, 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 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 a

drop

If TRUE and only one field is read, then a vector (rather than a single-column data.frame

verbose

An integer specifying the verbose level. If 0, the file is parsed quietly. The higher numbers, the more details.

Value

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

References

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

See Also

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

Examples

Run this code

##############################################################
if (require("AffymetrixDataTestFiles")) {            # START #
##############################################################

# Find any CDF file
cdfFile <- NULL
tryCatch({
  cdfFile <- findCdf()
}, error = function(ex) {})

if (!is.null(cdfFile)) {
  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))
}

##############################################################
}                                                     # STOP #
##############################################################

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