readCdfDataFrame {affxparser} | R Documentation |
Reads units (probesets) from an Affymetrix CDF file. Gets all or a subset of units (probesets).
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.
[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
().
############################################################## if (require("AffymetrixDataTestFiles")) { # START # ############################################################## # 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)) ############################################################## } # STOP # ##############################################################