chiptype.pdnn.params: Chip-type specific data
In affypdnn: Probe Dependent Nearest Neighbours (PDNN) for the affy package

Description Usage Format Details Note Source Examples

Chip-type specific data structure.

1	data(hgu95av2.pdnn.params)

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

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.

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

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

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## 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)