Cdf-class {makecdfenv} | R Documentation |
A class describing the content a Chip Description File.
The necessity for level
vectors associated with most of the
matrices arose from the following considerations. The name associated
to each probe is not unique, it corresponds to the gene name. It is
very common to have a name repeated 40 times (20 perfect matches and 20
mismatches). Using factor
objects allows to save memory, but we
also want to conserve the matrix structure. This was done by using of
the actual implementation of factor
objects: each level is
encoded with an integer. Probes can be grouped by pairs: a perfect
match (PM) probe has its mismatch (MM) counterpart. The two probes in a
pair differ by one base (usually located in the middle of the
sequence). The information relative to this particular base are stored
in pbase
and tbase
. At a given position (x,y), having
pbase[x,y] == tbase[x,y] means having a MM while having pbase[x,y] !=
tbase[x,y] means having a perfect mismatch if and only if one of the
bases is A while the other is TRUE, or one is G and the other is C. The
function
pmormm
returns TRUE
for PMs and FALSE
for
MMs.
new('Cdf',
cdfName = ...., # Object of class character
name = ...., # Object of class matrix
name.levels = ...., # Object of class character
pbase = ...., # Object of class matrix
pbase.levels = ...., # Object of class character
tbase = ...., # Object of class matrix
tbase.levels = ...., # Object of class character
atom = ...., # Object of class matrix
)
cdfName
:name
:name.levels
:name
.pbase
:pbase.levels
:pbase
. tbase
:tbase.levels
:tbase
. atom
:ato,
slot. atom
slot. name.levels
slot. name.levels
slot. pbase
slot. pbase
slot. pbase.levels
slot. pbase.levels
slot. tbase
slot. tbase
slot. tbase.levels
slot. tbase.levels
slot. L. Gautier <laurent@cbs.dtu.dk>
read.cdffile
,
make.cdf.env
,
make.cdf.package