Heat map plotting by genome coordinate

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Documentation for package ‘ChromHeatMap’ version 1.59.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ALLs.chr22	Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1
annotation-method	Class to contain data associated with chromosome coordinates across a whole genome.
chrdata	The ALLs.chr22 ExpressionSet, reformatted as a ChrStrandData object
chrHeatMap	Plot ChrStrandMatrix objects as heat maps along a chromosome
ChrMapPlot	Class containing a mapping between plot location and probe or gene identifier.
ChrMapPlot-class	Class containing a mapping between plot location and probe or gene identifier.
chrNames	Retrieve chromosome names from an object.
chrNames-method	Class to contain data associated with chromosome coordinates across a whole genome.
chrNames-method	Class to contain data associated with genome locations for a specific chromosome.
ChrStrandData	Class to contain data associated with chromosome coordinates across a whole genome.
ChrStrandData-class	Class to contain data associated with chromosome coordinates across a whole genome.
ChrStrandMatrix	Class to contain data associated with genome locations for a specific chromosome.
ChrStrandMatrix-class	Class to contain data associated with genome locations for a specific chromosome.
class:ChrMapPlot	Class containing a mapping between plot location and probe or gene identifier.
class:ChrStrandData	Class to contain data associated with chromosome coordinates across a whole genome.
class:ChrStrandMatrix	Class to contain data associated with genome locations for a specific chromosome.
createChrMatrix	Generate chromosome-based subset matrices from the mapped data structures generated by makeChrStrandData
cytobands	Cytoband location information
drawMapDendro	Draw a heatmap and dendrogram for a strand-specific data matrix generated by createChrMatrix
exprs-method	Class to contain data associated with genome locations for a specific chromosome.
featureNames-method	Class to contain data associated with genome locations for a specific chromosome.
grabChrMapProbes	Identify the probes or genes plotted using plotChrMap
makeChrStrandData	Map a data matrix onto chromosome coordinates
makeChrStrandData-method	Map a data matrix onto chromosome coordinates
makeChrStrandData-methods	Map a data matrix onto chromosome coordinates
makeRangedDataList	Plot expression data as tracks in the UCSC genome browser
plotChrMap	Plot data as an annotated heat map along a chromosome
sampleNames-method	Class to contain data associated with chromosome coordinates across a whole genome.
sampleNames-method	Class to contain data associated with genome locations for a specific chromosome.
show-method	Class containing a mapping between plot location and probe or gene identifier.
show-method	Class to contain data associated with chromosome coordinates across a whole genome.
show-method	Class to contain data associated with genome locations for a specific chromosome.
stains	Cytoband display information
strandName	Retrieve strand information from a ChrStrandMatrix object.
strandName-method	Class to contain data associated with genome locations for a specific chromosome.
summary-method	Class containing a mapping between plot location and probe or gene identifier.
summary-method	Class to contain data associated with chromosome coordinates across a whole genome.
summary-method	Class to contain data associated with genome locations for a specific chromosome.