readCdfCellIndices {affxparser} | R Documentation |
Reads cell indices of units (probesets) in an Affymetrix CDF file.
readCdfCellIndices(filename, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"), flat=FALSE, verbose=0)
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 vector s.
If "pm" /"mm" , only elements corresponding to
perfect-match (PM) / mismatch (MM) probes are returned (as vector s).
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. |
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". |
Henrik Bengtsson (http://www.braju.com/R/)
readCdfUnits
().