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ChromHeatMap (version 1.26.0)

Heat map plotting by genome coordinate

Description

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

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Version

Version

1.26.0

License

Artistic-2.0

Maintainer

Tim F Rayner

Last Published

February 15th, 2017

Functions in ChromHeatMap (1.26.0)

makeRangedDataList

Plot expression data as tracks in the UCSC genome browser
makeChrStrandData

Map a data matrix onto chromosome coordinates
ALLs.chr22

Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1
chrdata

The ALLs.chr22 ExpressionSet, reformatted as a ChrStrandData object
plotChrMap

Plot data as an annotated heat map along a chromosome
stains

Cytoband display information
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
ChrMapPlot

Class containing a mapping between plot location and probe or gene identifier.
chrHeatMap

Plot ChrStrandMatrix objects as heat maps along a chromosome
grabChrMapProbes

Identify the probes or genes plotted using plotChrMap
makeChrStrandData-methods

Map a data matrix onto chromosome coordinates
chrNames

Retrieve chromosome names from an object.
ChrStrandData

Class to contain data associated with chromosome coordinates across a whole genome.
cytobands

Cytoband location information
drawMapDendro

Draw a heatmap and dendrogram for a strand-specific data matrix generated by createChrMatrix
strandName

Retrieve strand information from a ChrStrandMatrix object.