\HeaderA{readCdfUnits}{Reads units (probesets) from an Affymetrix CDF file}{readCdfUnits}
\keyword{file}{readCdfUnits}
\keyword{IO}{readCdfUnits}
\begin{Description}\relax
Reads units (probesets) from an Affymetrix CDF file. Gets all or a subset of units (probesets).
\end{Description}
\begin{Usage}
\begin{verbatim}readCdfUnits(filename, units=NULL, readXY=TRUE, readBases=TRUE, readExpos=TRUE, readType=TRUE, readDirection=TRUE, stratifyBy=c("nothing", "pmmm", "pm", "mm"), readIndices=FALSE, verbose=0)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{filename}] The filename of the CDF file.
\item[\code{units}] An \code{\LinkA{integer}{integer}} \code{\LinkA{vector}{vector}} of unit indices
specifying which units to be read.  If \code{\LinkA{NULL}{NULL}}, all units are read.
\item[\code{readXY}] If \code{\LinkA{TRUE}{TRUE}}, cell row and column (x,y) coordinates are
retrieved, otherwise not.
\item[\code{readBases}] If \code{\LinkA{TRUE}{TRUE}}, cell P and T bases are retrieved, otherwise not.
\item[\code{readExpos}] If \code{\LinkA{TRUE}{TRUE}}, cell "expos" values are retrieved, otherwise not.
\item[\code{readType}] If \code{\LinkA{TRUE}{TRUE}}, unit types are retrieved, otherwise not.
\item[\code{readDirection}] If \code{\LinkA{TRUE}{TRUE}}, unit directions are retrieved, otherwise not.
\item[\code{stratifyBy}] A \code{\LinkA{character}{character}} string specifying which and how
elements in group fields are returned.
If \code{"nothing"}, elements are returned as is, i.e. as \code{\LinkA{vector}{vector}}s.
If \code{"pm"}/\code{"mm"}, only elements corresponding to
perfect-match (PM) / mismatch (MM) probes are returned (as \code{\LinkA{vector}{vector}}s).
If \code{"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.
\item[\code{readIndices}] If \code{\LinkA{TRUE}{TRUE}}, cell indices calculated from the row and
column (X,Y) coordinates are retrieved, otherwise not.
\item[\code{verbose}] An \code{\LinkA{integer}{integer}} specifying the verbose level. If 0, the
file is parsed quietly.  The higher numbers, the more details.
\end{ldescription}
\end{Arguments}
\begin{Value}
A named \code{\LinkA{list}{list}} where the names corresponds to the names
of the units read.  Each element of the list is in turn a
\code{\LinkA{list}{list}} structure with three components:
\begin{ldescription}
\item[\code{groups}] A \code{\LinkA{list}{list}} with one component for each group
(also called block). The information on each group is a
\code{\LinkA{list}{list}} with five components: \code{x}, \code{y},
\code{pbase}, \code{tbase}, \code{expos}, and \code{indices}.
\item[\code{type}] An \code{\LinkA{integer}{integer}} specifying the type of the
unit, where 1 is "expression", 2 is "genotyping", 3 is "CustomSeq",
and 4 "tag".
\item[\code{direction}] An \code{\LinkA{integer}{integer}} specifying the direction
of the unit, which defines if the probes are interrogating the sense
or the anti-sense target, where 0 is "no direction", 1 is "sense", and
2 is "anti-sense".
\end{ldescription}
\end{Value}
\begin{Author}\relax
James Bullard, \email{bullard@stat.berkeley.edu} and Kasper
Daniel Hansen, \email{khansen@stat.berkeley.edu}.
Modified by Henrik Bengtsson (\url{http://www.braju.com/R/}) to read
any subset of units and/or subset of parameters, to stratify by PM/MM,
and to return cell indices.d
\end{Author}
\begin{References}\relax
[1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats,
June 14, 2005.
\url{http://www.affymetrix.com/support/developer/}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{readCdfCellIndices}{readCdfCellIndices}}().
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

for (zzz in 0) {

# Find any CDF file
cdfFile <- findCdf()
if (is.null(cdfFile))
  break

# Read all units in a CDF file [~20s => 0.34ms/unit]
cdf0 <- readCdfUnits(cdfFile, readXY=FALSE, readExpos=FALSE)

# Read a subset of units in a CDF file [~6ms => 0.06ms/unit]
units1 <- c(5, 100:109, 34)
cdf1 <- readCdfUnits(cdfFile, units=units1, readXY=FALSE, readExpos=FALSE)
stopifnot(identical(cdf1, cdf0[units1]))
rm(cdf0)

# Create a unit name to index map
names <- readCdfUnitNames(cdfFile)
units2 <- match(names(cdf1), names)
stopifnot(all.equal(units1, units2))
cdf2 <- readCdfUnits(cdfFile, units=units2, readXY=FALSE, readExpos=FALSE)

stopifnot(identical(cdf1, cdf2))

# Clean up
rm(cdfFile, units1, cdf1, names, units2, cdf2)

} # for (zzz in 0)
\end{ExampleCode}
\end{Examples}

