Heat map plotting by genome coordinate


[Package List] [Top]

Documentation for package ‘ChromHeatMap’ version 1.0.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

ALLs.chr22 Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1
annotation,ChrStrandData-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 identifier.
ChrMapPlot-class Class containing a mapping between plot location and probe identifier.
chrNames Retrieve chromosome names from an object.
chrNames,ChrStrandData-method Class to contain data associated with chromosome coordinates across a whole genome.
chrNames,ChrStrandMatrix-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 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,ChrStrandMatrix-method Class to contain data associated with genome locations for a specific chromosome.
featureNames,ChrStrandMatrix-method Class to contain data associated with genome locations for a specific chromosome.
grabChrMapProbes Identify the probes plotted using plotChrMap
makeChrStrandData Map a data matrix onto chromosome coordinates
makeChrStrandData,ExpressionSet-method Map a data matrix onto chromosome coordinates
makeChrStrandData,matrix-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,ChrStrandData-method Class to contain data associated with chromosome coordinates across a whole genome.
sampleNames,ChrStrandMatrix-method Class to contain data associated with genome locations for a specific chromosome.
show,ChrMapPlot-method Class containing a mapping between plot location and probe identifier.
show,ChrStrandData-method Class to contain data associated with chromosome coordinates across a whole genome.
show,ChrStrandMatrix-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,ChrStrandMatrix-method Class to contain data associated with genome locations for a specific chromosome.
summary,ChrMapPlot-method Class containing a mapping between plot location and probe identifier.
summary,ChrStrandData-method Class to contain data associated with chromosome coordinates across a whole genome.
summary,ChrStrandMatrix-method Class to contain data associated with genome locations for a specific chromosome.