pdnn.params.chiptype {affypdnn} | R Documentation |
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 |
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.
energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u95av2.txt", package="affypdnn") params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack="hgu95av2probe")