comparisonPlot

list of numeric vector, each of same length as <code>x</code>.

xscale

matrix with 2 rows and columns corresponding to the
    elements of <code>x</code>.

yscale

dataframe with columns <code>start</code>, <code>end</code>, and
    <code>name</code>, each row corresponds to one gene CDS to be plotted at the bottom.

anno

ticks

A numeric or character vector indicating what sort of
    plotting symbol to use, see <code><a rd-options="grid" href="/link/grid.points?package=tilingArray&version=1.50.0&to=grid" data-mini-rdoc="grid::grid.points">grid.points</a></code>.

Multiplier applied to fontsize, see <code><a rd-options="grid" href="/link/gpar?package=tilingArray&version=1.50.0&to=grid" data-mini-rdoc="grid::gpar">gpar</a></code>.

Color to use as background for some of the plot panels.

bgcol


  This function is used for Figure 5 in the David et al. (PNAS 2006)
  paper and in the Huber et al. methods paper.


manip

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

comparisonPlot function

A numeric or character vector indicating what sort of
    plotting symbol to use, see <code><a href="grid.points" rd-options="grid">grid.points</a></code>.

Multiplier applied to fontsize, see <code><a href="gpar" rd-options="grid">gpar</a></code>.

This function is used for Figure 5 in the David et al. (PNAS 2006)
  paper and in the Huber et al. methods paper.

comparisonPlot: Plot a vertical layout of panels for the comparison of different along-chromosome profiles.

Description

Usage

Arguments

Value

References

Examples