pdnn.params.chiptype {affypdnn}R Documentation

A function to fit PDNN parameters


A function to fit PDNN parameters that are chip-type specific


pdnn.params.chiptype(energy.param.file, probes.file = NULL, probes.pack= NULL,
                     probes.data.frame = NULL,
                     seq.name, x.name, y.name, affyid.name, verbose = TRUE)


energy.param.file Path to the energy data file (see details)
probes.file Path to the probe files (see details)
probes.pack Name of the probe pack (see details)
probes.data.frame A data.frame
seq.name, x.name, y.name, affyid.name The names of the columns in the data.frame from probes.pack or probes.file for the probe sequences, the X positions, the Y positions and the probe set ID respectively
verbose verbosity (TRUE or FALSE


The parameters probes.file, probes.pack and probes.data.frame are mutually exclusive. The function fits PDNN parameters that are specific to chip-types (hence specific to the probe sequences). It requires data files like the one found on Li Zhang's web page: (http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/) This should be computed once for all for a given chip type. Computed values for the chips are included in the package. This allows 'automagic' use of them when these chips types are used (as done in the function expressopdnn).


A list of:

Eg environment. One entry per dinucleotide.
Wg numerical vector
En environment. One entry per dinucleotide.
Wn numerical vector
params.gene environment. One entry per gene, each entry is is a list of elements Sg, Sn, xy and gene.i

See Also



if (interactive()) {
  energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u95av2.txt", package="affypdnn")

  params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack="hgu95av2probe")

[Package affypdnn version 1.1-0 Index]