affxparser (version 1.44.0)

readCdfUnits: 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

readCdfUnits(filename, units=NULL, readXY=TRUE, readBases=TRUE, readExpos=TRUE, readType=TRUE, readDirection=TRUE, stratifyBy=c("nothing", "pmmm", "pm", "mm"), readIndices=FALSE, 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 units are read.

readXY

If TRUE, cell row and column (x,y) coordinates are retrieved, otherwise not.

readBases

If TRUE, cell P and T bases are retrieved, otherwise not.

readExpos

If TRUE, cell "expos" values are retrieved, otherwise not.

readType

If TRUE, unit types are retrieved, otherwise not.

readDirection

If TRUE, unit and group directions are retrieved, otherwise not.

stratifyBy

A 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.

readIndices

If TRUE, cell indices calculated from the row and column (x,y) coordinates are retrieved, otherwise not. Note that these indices are one-based.

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:

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: 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.

type

An integer specifying the type of the unit, where 1 is "expression", 2 is "genotyping", 3 is "CustomSeq", and 4 "tag".

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".

Cell indices are one-based

Note that in affxparser all cell indices are by convention one-based, which is more convenient to work with in R. For more details on one-based indices, see 2. Cell coordinates and cell indices.

References

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

See Also

readCdfCellIndices().

Examples

##############################################################
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 #
##############################################################