#########################################################################/**
# @RdocFunction readCdfUnits
#
# @title "Reads units (probesets) from an Affymetrix CDF file"
#
# @synopsis
#
# \description{
# @get "title". Gets all or a subset of units (probesets).
# }
#
# \arguments{
# \item{filename}{The filename of the CDF file.}
# \item{units}{An @integer @vector of unit indices
# specifying which units to be read. If @NULL, all units are read.}
# \item{readXY}{If @TRUE, cell row and column (x,y) coordinates are
# retrieved, otherwise not.}
# \item{readBases}{If @TRUE, cell P and T bases are retrieved, otherwise not.}
# \item{readExpos}{If @TRUE, cell "expos" values are retrieved, otherwise not.}
# \item{readType}{If @TRUE, unit types are retrieved, otherwise not.}
# \item{readDirection}{If @TRUE, unit \emph{and} group directions are
# retrieved, otherwise not.}
# \item{stratifyBy}{A @character string specifying which and how
# elements in group fields are returned.
# If \code{"nothing"}, elements are returned as is, i.e. as @vectors.
# If \code{"pm"}/\code{"mm"}, only elements corresponding to
# perfect-match (PM) / mismatch (MM) probes are returned (as @vectors).
# 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{readIndices}{If @TRUE, cell indices \emph{calculated} from
# the row and column (x,y) coordinates are retrieved, otherwise not.
# Note that these indices are \emph{one-based}.}
# \item{verbose}{An @integer specifying the verbose level. If 0, the
# file is parsed quietly. The higher numbers, the more details.}
# }
#
# \value{
# A named @list where the names corresponds to the names
# of the units read. Each element of the list is in turn a
# @list structure with three components:
# \item{groups}{A @list with one component for each group
# (also called block). The information on each group is a
# @list of up to seven components: \code{x}, \code{y},
# \code{pbase}, \code{tbase}, \code{expos}, \code{indices},
# and \code{direction}.
# All fields but the latter have the same number of values as
# there are cells in the group. The latter field has only
# one value indicating the direction for the whole group.
# }
# \item{type}{An @integer specifying the type of the
# unit, where 1 is "expression", 2 is "genotyping", 3 is "CustomSeq",
# and 4 "tag".}
# \item{direction}{An @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".}
# }
#
# \section{Cell indices are one-based}{
# Note that in \pkg{affxparser} all \emph{cell indices} are by
# convention \emph{one-based}, which is more convenient to work
# with in \R. For more details on one-based indices, see
# @see "2. Cell coordinates and cell indices".
# }
#
# \author{
# James Bullard and Kasper Daniel Hansen.
# Modified by Henrik Bengtsson to read any subset of units and/or subset of
# parameters, to stratify by PM/MM, and to return cell indices.
# }
#
# @examples "../incl/readCdfUnits.Rex"
#
# \seealso{
# @see "readCdfCellIndices".
# }
#
# \references{
# [1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats,
# June 14, 2005.
# \url{http://www.affymetrix.com/support/developer/}
# }
#
# @keyword "file"
# @keyword "IO"
#*/#########################################################################
readCdfUnits <- function(filename, units=NULL, readXY=TRUE, readBases=TRUE, readExpos=TRUE, readType=TRUE, readDirection=TRUE, stratifyBy=c("nothing", "pmmm", "pm", "mm"), readIndices=FALSE, verbose=0) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Validate arguments
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Argument 'filename':
filename <- file.path(dirname(filename), basename(filename));
if (!file.exists(filename))
stop("File not found: ", filename);
# Argument 'units':
if (is.null(units)) {
} else if (is.numeric(units)) {
units <- as.integer(units);
if (any(units < 1))
stop("Argument 'units' contains non-positive indices.");
} else {
stop("Argument 'units' must be numeric or NULL: ", class(units)[1]);
}
# Argument 'verbose':
if (length(verbose) != 1)
stop("Argument 'verbose' must be a single integer.");
verbose <- as.integer(verbose);
if (!is.finite(verbose))
stop("Argument 'verbose' must be an integer: ", verbose);
# Argument 'readXY':
readXY <- as.integer(as.logical(readXY));
# Argument 'readBases':
readBases <- as.integer(as.logical(readBases));
# Argument 'readExpos':
readExpos <- as.integer(as.logical(readExpos));
# Argument 'readType':
readType <- as.integer(as.logical(readType));
# Argument 'readDirection':
readDirection <- as.integer(as.logical(readDirection));
# Argument 'stratifyBy':
stratifyBy <- match.arg(stratifyBy);
# Argument 'readIndices':
readIndices <- as.integer(as.logical(readIndices));
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Read the CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# UNSUPPORTED CASE?
if (!is.null(units) && length(units) == 0L) {
stop("readCdfUnits(..., units=integer(0)) is not supported.")
}
cdf <- .Call("R_affx_get_cdf_units", filename, units,
readXY, readBases, readExpos,
readType, readDirection,
readIndices,
verbose, PACKAGE="affxparser");
# Sanity check
if (is.null(cdf)) {
stop("Failed to read CDF file: ", filename);
}
if (stratifyBy == "nothing")
return(cdf);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Stratify by PM, MM, or PM & MM
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
isPm <- readCdfIsPm(filename, units=units);
# Using .subset2() instead of "[["() to avoid dispatching overhead etc.
if (stratifyBy == "pmmm") {
dimnames <- list(c("pm", "mm"), NULL);
for (uu in seq_along(cdf)) {
# groups <- cdf[[uu]]$groups;
groups <- .subset2(.subset2(cdf, uu), "groups");
ngroups <- length(groups);
if (ngroups == 0)
next;
for (gg in 1:ngroups) {
# group <- groups[[gg]];
group <- .subset2(groups, gg);
# pm <- isPm[[uu]][[gg]];
pm <- .subset2(.subset2(isPm, uu), gg);
idx <- 1:length(pm);
mm <- idx[!pm]; # Note: which(!pm) is about 60% slower! /HB
pm <- idx[pm];
npm <- length(pm);
if (npm != length(mm)) {
# This is not expected to happen, but just in case.
stop("Number of PM and MM probes differ in probeset #", uu,
": ", length(pm), " != ", length(mm));
}
pmmm <- matrix(c(pm, mm), nrow=2L, ncol=npm, byrow=TRUE);
# dimnames(pmmm) <- dimnames;
# Re-order cell elements according to PM/MM.
ngroup <- length(group);
if (ngroup > 0) {
dim <- c(2, npm);
for (kk in 1:ngroup) {
# value <- group[[kk]][pmmm];
value <- .subset(.subset2(group, kk), pmmm);
dim(value) <- dim;
dimnames(value) <- dimnames;
group[[kk]] <- value;
}
}
# group[["pmmm"]] <- pmmm;
groups[[gg]] <- group;
} # for (gg ...)
cdf[[uu]]$groups <- groups;
} # for (uu ...)
} else if (stratifyBy == "pm") {
for (uu in seq_along(cdf)) {
groups <- cdf[[uu]]$groups;
ngroups <- length(groups);
if (ngroups == 0)
next;
for (gg in 1:ngroups) {
group <- groups[[gg]];
ngroup <- length(group);
if (ngroup == 0)
next;
pm <- .subset2(.subset2(isPm, uu), gg);
pm <- (1:length(pm))[pm]; # Note: which(!pm) is about 60% slower!
for (kk in 1:ngroup) {
group[[kk]] <- .subset(.subset2(group, kk), pm);
}
groups[[gg]] <- group;
} # for (gg ...)
cdf[[uu]]$groups <- groups;
} # for (uu ...)
} else if (stratifyBy == "mm") {
for (uu in seq_along(cdf)) {
groups <- cdf[[uu]]$groups;
ngroups <- length(groups);
if (ngroups == 0)
next;
for (gg in 1:ngroups) {
group <- groups[[gg]];
ngroup <- length(group);
if (ngroup == 0)
next;
pm <- .subset2(.subset2(isPm, uu), gg);
mm <- (1:length(pm))[!pm]; # Note: which(!pm) is about 60% slower!
for (kk in 1:ngroup) {
group[[kk]] <- .subset(.subset2(group, kk), mm);
}
groups[[gg]] <- group;
} # for (gg ...)
cdf[[uu]]$groups <- groups;
} # for (uu ...)
}
cdf;
} # readCdfUnits()
############################################################################
# HISTORY:
# 2011-11-18
# o ROBUSTNESS: Added sanity check that the native code did not return NULL.
# 2011-02-15
# o DOCUMENTATION: Clarified in help(readCdfUnits) that (x,y) coordinates
# are zero-based and the _from (x,y) calculated_ cell indices are
# one-based, regardless what the indices on file are.
# 2010-12-12
# o ROBUSTNESS: Replaces .Internal(matrix(...)) with matrix().
# In the upcoming R 2.13.0 matrix() has less overhead.
# 2006-12-30
# o Now 'readDirection=TRUE' also return group directions.
# 2006-03-28
# o Unit indices are now one-based. /HB
# o Renamed argument 'readCells' to 'readIndices'. /HB
# 2006-03-24
# o Not returning 'pmmm' field anymore. A bit faster an smaller object.
# o Speed improvement of the "stratifyBy" code. Instead of using which()
# one can do the same oneself, which is 50% faster. In addition, I have
# replaced "[[" and "[" with .subset2() and .subset().
# 2006-02-21
# o Added argument 'readCells' to speed up the calculation of cell indices
# from (x,y), i.e. cell = y * ncol + x.
# o Replaced argument 'splitPmMm' with 'stratifyBy'. This will speed up
# things down the stream.
# 2006-01-16
# o Added argument 'splitPmMm'. /HB
# 2006-01-09
# o Note that ../man/readCdfUnits.R in generated from the Rdoc comments
# above. See the R.oo package for details. Don't remove the *.Rex files!
# o Created by HB. The purpose was to make it possible to read subsets
# of units and not just all units at once. /HB
############################################################################
