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ChromHeatMap (version 1.24.0)

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

1.24.0

License

Artistic-2.0

Maintainer

Tim F Rayner

Last Published

February 15th, 2017

Functions in ChromHeatMap (1.24.0)

cytobands

Cytoband location information
chrNames

Retrieve chromosome names from an object.
ChrStrandData

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

Map a data matrix onto chromosome coordinates
makeRangedDataList

Plot expression data as tracks in the UCSC genome browser
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
drawMapDendro

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

Retrieve strand information from a ChrStrandMatrix object.
chrHeatMap

Plot ChrStrandMatrix objects as heat maps along a chromosome
ChrMapPlot

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

Cytoband display information
plotChrMap

Plot data as an annotated heat map along a chromosome
ALLs.chr22

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

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

Identify the probes or genes plotted using plotChrMap
makeChrStrandData-methods

Map a data matrix onto chromosome coordinates