residuals.breakpointsPretend

breakpoints.breakpointsPretend

object

breaks


  Accessor methods for breakpointsPretend objects - not to be called
  by the user.<p></p><p>  These functions are used in the interface between the
  <code>segmentation</code> class and the
  <code><a rd-options="strucchange:confint.breakpointsfull" href="/link/confint.breakpointsfull?package=tilingArray&version=1.50.0&to=strucchange%3Aconfint.breakpointsfull" data-mini-rdoc="strucchange:confint.breakpointsfull::confint.breakpointsfull">confint.breakpointsfull</a></code>
  method of the strucchange package. This method calls
  <code>breakpoints</code> and <code>residuals</code> methods for its first
  argument, and since we pass an argument of S3 class
  <code>breakpointsPretend</code>, we can avoid the overhead of the
  corresponding methods for <code>breakpointsfull</code> objects.
  These functions are of no interest to the user.
</p>

manip

breakpointsPretend

The package provides functionality that can be
useful for the analysis of high-density tiling microarray data (such
as from Affymetrix genechips) for measuring transcript abundance and
architecture. The main functionalities of the package are: 1. the class
'segmentation' for representing partitionings of a linear series of
data; 2. the function 'segment' for fitting piecewise constant models
using a dynamic programming algorithm that is both fast and exact; 3.
the function 'confint' for calculating confidence intervals using the
strucchange package; 4. the function 'plotAlongChrom' for generating
pretty plots; 5. the function 'normalizeByReference' for probe-sequence
dependent response adjustment from a (set of) reference
hybridizations.

Zhenyu Xu

tilingArray

Transcript mapping with high-density oligonucleotide tiling arrays

breakpointsPretend function

Accessor methods for breakpointsPretend objects - not to be called
  by the user.

  These functions are used in the interface between the
  <code>segmentation</code> class and the
  <code><a href="confint.breakpointsfull" rd-options="strucchange:confint.breakpointsfull">confint.breakpointsfull</a></code>
  method of the strucchange package. This method calls
  <code>breakpoints</code> and <code>residuals</code> methods for its first
  argument, and since we pass an argument of S3 class
  <code>breakpointsPretend</code>, we can avoid the overhead of the
  corresponding methods for <code>breakpointsfull</code> objects.
  These functions are of no interest to the user.

breakpointsPretend: Accessor methods for breakpointsPretend objects - not to be called by the user.

Description

Usage

Arguments

Value