affy (version 1.50.0)

pdnn.params.chiptype: A function to fit PDNN parameters

Description

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

Usage

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)

Arguments

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)

Value

• 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

warning

The X and Y positions in the data.frame are expected to be original ones in the Affymetrix files (starting at zero. They are offset by one within this function.

Details

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).

See Also

find.params.pdnn

Examples

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")
}