hgu133a.pdnn.params {affypdnn} | R Documentation

## Chip-type specific data

### Description

Chip-type specific data structure.

### Usage

    data(hgu95av2.pdnn.params)

### Format

The format is a list:

Eg

  environment (one entry per dinucleotide)

Wg

  numerical vector.

En

  environment (one entry per dinucleotide)

Wn

  numerical vector.

gene.Sn

  list (one entry per affyID)

gene.Sg

  list (one entry per affyID)

gene.xy

  list (one entry per affyID)

params.gene

  environment

### Details

These chip-specific data structures are generated from the data files made available by the author of the PDNN paper (see the section source). They are stored as `data` to save some computation time. The data structures were made using the function `pdnn.params.chiptype`. The data files are included in the the directory ‘data’ of the package.

### Note

To lower the size of the package, the only chip-specific data structures included in the package is the one for HG-U95Av2.

### Source

Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of molecular interactions on short oligonucleotide arrays, 2003, Nature Biotech., vol. 21, n.7

### Examples

    ## give the path the original energy parameter files included in the package
    list.files(system.file("exampleData", package="affypdnn"),
               "^pdnn-energy-parameter_", full.names=TRUE)

[Package affypdnn version 1.60.0 Index]