pdnn.params.chiptype: A function to fit PDNN parameters
In affypdnn: Probe Dependent Nearest Neighbours (PDNN) for the affy package

Description Usage Arguments Details Value warning See Also Examples

View source: R/pdnn.params.chiptype.R

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

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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

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.

find.params.pdnn

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")
}