The ChromosomalModel class

Share:

Description

Package: aroma.core
Class ChromosomalModel

Object
~~|
~~+--ChromosomalModel

Directly known subclasses:
CbsModel, CopyNumberChromosomalModel, CopyNumberSegmentationModel, GladModel, HaarSegModel, RawCopyNumberModel

public abstract static class ChromosomalModel
extends Object

This abstract class represents a chromosomal model.

Usage

1
ChromosomalModel(cesTuple=NULL, tags="*", genome="Human", chromosomes=NULL, ...)

Arguments

cesTuple

A AromaMicroarrayDataSetTuple.

tags

A character vector of tags.

genome

A character string specifying what genome is process.

chromosomes

(optional) A vector specifying which chromosomes to process.

...

Not used.

Fields and Methods

Methods:

fit -
getChipType Gets a label for all chip types merged.
getChipTypes -
getChromosomes Gets the chromosomes to be processed.
getFullName -
getFullNames -
getGenome -
getName -
getNames Gets the names of the arrays.
getPath -
getSets -
getTags -
indexOf -
nbrOfArrays Gets the number of arrays.
nbrOfChipTypes Gets the number of chip types.
setChromosomes -
setGenome -

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis

Requirements

This class requires genome information annotation files for every chip type.

Author(s)

Henrik Bengtsson

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.