readCdfCellIndices {affxparser}R Documentation

Reads cell indices of units (probesets) in an Affymetrix CDF file

Description

Reads cell indices of units (probesets) in an Affymetrix CDF file.

Usage

readCdfCellIndices(filename, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"), flat=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.
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.
flat Do we want a flat return.
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 with five components: x, y, pbase, tbase, expos, and indices.
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".

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

readCdfUnits().


[Package affxparser version 1.4.1 Index]