Heat map plotting by genome coordinate


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Documentation for package ‘ChromHeatMap’ version 1.4.0

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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
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
ChrMapPlot-class Class containing a mapping between plot location and probe or gene
chrNames Retrieve chromosome names from an object.
chrNames-method Class to contain data associated with chromosome coordinates across a
chrNames-method Class to contain data associated with genome locations for a specific
ChrStrandData Class to contain data associated with chromosome coordinates across a
ChrStrandData-class Class to contain data associated with chromosome coordinates across a
ChrStrandMatrix Class to contain data associated with genome locations for a specific
ChrStrandMatrix-class Class to contain data associated with genome locations for a specific
class:ChrMapPlot Class containing a mapping between plot location and probe or gene
class:ChrStrandData Class to contain data associated with chromosome coordinates across a
class:ChrStrandMatrix Class to contain data associated with genome locations for a specific
createChrMatrix Generate chromosome-based subset matrices from the mapped data
cytobands Cytoband location information
drawMapDendro Draw a heatmap and dendrogram for a strand-specific data matrix
exprs-method Class to contain data associated with genome locations for a specific
featureNames-method Class to contain data associated with genome locations for a specific
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
sampleNames-method Class to contain data associated with genome locations for a specific
show-method Class containing a mapping between plot location and probe or gene
show-method Class to contain data associated with chromosome coordinates across a
show-method Class to contain data associated with genome locations for a specific
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
summary-method Class containing a mapping between plot location and probe or gene
summary-method Class to contain data associated with chromosome coordinates across a
summary-method Class to contain data associated with genome locations for a specific