singleclusterplot

an items x columns matrix with numerical entries. each item will define a line in the clusterplot

cluster

if multiple clusters should be plotted in one diagram, the cluster labels for each item are given in this vector

label

at which x-positions will the columns occur in the plot?

main

xlim

x-axis legend, standard graphics parameter 

xlab

should an x axis be plotted at all? (="n" if not)

xaxt

xlabels

las=1: horizontal text, la2=2: vertical text

ylim

y-axis legend, standard graphics parameter

ylab

fromto

either "red","green","blue" (standard colors), or a vector of colors that can be used instead of a standard color palette.

colpal

how many colors will the color palette contain?

nrcolors

outer.col

should the quartile lines be plotted (grey/black)?

add.quartiles

internal

Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.

singleclusterplot: single cluster plot

Description

Usage

Arguments