readCelUnits: Reads probe-level data ordered as units (probesets) from one...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/readCelUnits.R

Description

Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files by using the unit and group definitions in the corresponding Affymetrix CDF file.

Usage

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readCelUnits(filenames, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"),
  cdf=NULL, ..., addDimnames=FALSE, dropArrayDim=TRUE, transforms=NULL, readMap=NULL,
  verbose=FALSE)

Arguments

filenames

The filenames of the CEL files.

units

An integer vector of unit indices specifying which units to be read. If NULL, all units are read.

stratifyBy

Argument passed to low-level method readCdfCellIndices.

cdf

A character filename of a CDF file, or a CDF list structure. If NULL, the CDF file is searched for by findCdf() first starting from the current directory and then from the directory where the first CEL file is.

...

Arguments passed to low-level method readCel, e.g. readXY and readStdvs.

addDimnames

If TRUE, dimension names are added to arrays, otherwise not. The size of the returned CEL structure in bytes increases by 30-40% with dimension names.

dropArrayDim

If TRUE and only one array is read, the elements of the group field do not have an array dimension.

transforms

A list of exactly length(filenames) functions. If NULL, no transformation is performed. Intensities read are passed through the corresponding transform function before being returned.

readMap

A vector remapping cell indices to file indices. If NULL, no mapping is used.

verbose

Either a logical, a numeric, or a Verbose object specifying how much verbose/debug information is written to standard output. If a Verbose object, how detailed the information is is specified by the threshold level of the object. If a numeric, the value is used to set the threshold of a new Verbose object. If TRUE, the threshold is set to -1 (minimal). If FALSE, no output is written (and neither is the R.utils package required).

Value

A named list with one element for each unit read. The names corresponds to the names of the units read. Each unit element is in turn a list structure with groups (aka blocks). Each group contains requested fields, e.g. intensities, stdvs, and pixels. If more than one CEL file is read, an extra dimension is added to each of the fields corresponding, which can be used to subset by CEL file.

Note that neither CEL headers nor information about outliers and masked cells are returned. To access these, use readCelHeader() and readCel().

Author(s)

Henrik Bengtsson

References

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

See Also

Internally, readCelHeader(), readCdfUnits() and readCel() are used.

Examples

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##############################################################
if (require("AffymetrixDataTestFiles")) {            # START #
##############################################################

# Search for some available CEL files
path <- system.file("rawData", package="AffymetrixDataTestFiles")
files <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE, firstOnly=FALSE)
files <- grep("FusionSDK_Test3", files, value=TRUE)
files <- grep("Calvin", files, value=TRUE)

# Fake more CEL files if not enough
files <- rep(files, length.out=5)
print(files);
rm(files);


##############################################################
}                                                     # STOP #
##############################################################

affxparser documentation built on Nov. 1, 2018, 2:25 a.m.