Cdf-class {makecdfenv} | R Documentation

## Class Cdf

### Description

A class describing the content a Chip Description File.

### Details

The class `Cdf` was designed to store the content of Affymetrix's Chip Definition Files (CDF). This early class is no longer widely used in the package affy. Environments (called `cdfenvs`) are preferred to have an efficient mapping between probe set identifiers and indexes (needed to access/subset particular probe intensities). Unless one needs to access every information contained in a CDF file, the `cdfenvs` will be preferred.

The following comments are only relevant to someone with interest in what is in a CDF file. 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). 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.

To know more about the file structure of a CDF file, one has to refer to the parsing code (mostly in C).

### Creating Objects

`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`
`)`

### Slots

`cdfName`:
  the CDF name tag. Used to link with the right CEL files
`name`:
  Object of class "matrix" of 'factors' for the gene names corresponding to the probes.
`name.levels`:
  Object of class "character" containing the levels corresponding to `name`.
`pbase`:
  Object of class "matrix" of pbase levels.
`pbase.levels`:
  Object of class "character" containing the levels corresponding to `pbase`.
`tbase`:
  Object of class "matrix" of tbase levels.
`tbase.levels`:
  Object of class "character" containing the levels corresponding to `tbase`.
`atom`:
  Object of class "matrix" of atom or probe numbers.

### Methods

atom
  (Cdf): An accesor function for the `ato,` slot.
atom<-
  (Cdf): A replacement function for `atom` slot.
name.levels
  (Cdf): An accesor function for the `name.levels` slot.
name.levels<-
  (Cdf): A replacement function for `name.levels` slot.
pbase
  (Cdf): An accesor function for the `pbase` slot.
pbase<-
  (Cdf): A replacement function for `pbase` slot.
pbase.levels
  (Cdf): An accesor function for the `pbase.levels` slot.
pbase.levels<-
  (Cdf): A replacement function for `pbase.levels` slot.
show
  (Cdf): renders information about the exprSet in a concise way on stdout.
tbase
  (Cdf): An accesor function for the `tbase` slot.
tbase<-
  (Cdf): A replacement function for `tbase` slot.
tbase.levels
  (Cdf): An accesor function for the `tbase.levels` slot.
tbase.levels<-
  (Cdf): A replacement function for `tbase.levels` slot.

### Author(s)

L. Gautier <laurent@cbs.dtu.dk>

### See Also

`read.cdffile`, `make.cdf.env`, `make.cdf.package`

[Package makecdfenv version 1.10.0 Index]