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readCdfUnits(filename, units=NULL, readXY=TRUE, readBases=TRUE, readExpos=TRUE, readType=TRUE, readDirection=TRUE, stratifyBy=c("nothing", "pmmm", "pm", "mm"), readIndices=FALSE, verbose=0)TRUE, cell row and column (x,y) coordinates are
retrieved, otherwise not.TRUE, cell P and T bases are retrieved, otherwise not.TRUE, cell "expos" values are retrieved, otherwise not.TRUE, unit types are retrieved, otherwise not.TRUE, unit and group directions are
retrieved, otherwise not.character string specifying which and how
elements in group fields are returned.
If "nothing", elements are returned as is, i.e. as vectors.
If "pm"/"mm", only elements corresponding to
perfect-match (PM) / mismatch (MM) probes are returned (as vectors).
If "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.TRUE, cell indices calculated from
the row and column (x,y) coordinates are retrieved, otherwise not.
Note that these indices are one-based.integer specifying the verbose level. If 0, the
file is parsed quietly. The higher numbers, the more details.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:
list with one component for each group
(also called block). The information on each group is a
list of up to seven components: x, y,
pbase, tbase, expos, indices,
and 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.
integer specifying the type of the
unit, where 1 is "expression", 2 is "genotyping", 3 is "CustomSeq",
and 4 "tag".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".2. Cell coordinates and cell indices.readCdfCellIndices().
##############################################################
if (require("AffymetrixDataTestFiles")) { # START #
##############################################################
# Find any CDF file
cdfFile <- findCdf()
# 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))
##############################################################
} # STOP #
##############################################################
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