ChromHeatMap: Heat map plotting by genome coordinate

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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.

Author
Tim F. Rayner
Date of publication
None
Maintainer
Tim F. Rayner <tfrayner@gmail.com>
License
Artistic-2.0
Version
1.28.0

View on Bioconductor

Man pages

ALLs.chr22
Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1
chrdata
The ALLs.chr22 ExpressionSet, reformatted as a ChrStrandData...
chrHeatMap
Plot ChrStrandMatrix objects as heat maps along a chromosome
ChrMapPlot-class
Class containing a mapping between plot location and probe or...
chrNames
Retrieve chromosome names from an object.
ChrStrandData-class
Class to contain data associated with chromosome coordinates...
ChrStrandMatrix-class
Class to contain data associated with genome locations for a...
createChrMatrix
Generate chromosome-based subset matrices from the mapped...
cytobands
Cytoband location information
drawMapDendro
Draw a heatmap and dendrogram for a strand-specific data...
grabChrMapProbes
Identify the probes or genes plotted using plotChrMap
makeChrStrandData
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
stains
Cytoband display information
strandName
Retrieve strand information from a ChrStrandMatrix object.

Files in this package

ChromHeatMap/DESCRIPTION
ChromHeatMap/NAMESPACE
ChromHeatMap/R
ChromHeatMap/R/ChrMapPlot-class.R
ChromHeatMap/R/ChrStrandData-class.R
ChromHeatMap/R/ChrStrandMatrix-class.R
ChromHeatMap/R/chrHeatMap.R
ChromHeatMap/R/createChrMatrix.R
ChromHeatMap/R/drawMapDendro.R
ChromHeatMap/R/grabChrMapProbes.R
ChromHeatMap/R/makeChrStrandData.R
ChromHeatMap/R/makeRangedDataList.R
ChromHeatMap/R/paintCytoBands.R
ChromHeatMap/R/plotChrMap.R
ChromHeatMap/build
ChromHeatMap/build/vignette.rds
ChromHeatMap/data
ChromHeatMap/data/cytobands.rda
ChromHeatMap/data/demo.rda
ChromHeatMap/inst
ChromHeatMap/inst/doc
ChromHeatMap/inst/doc/ChromHeatMap.R
ChromHeatMap/inst/doc/ChromHeatMap.Rnw
ChromHeatMap/inst/doc/ChromHeatMap.pdf
ChromHeatMap/man
ChromHeatMap/man/ALLs.chr22.Rd
ChromHeatMap/man/ChrMapPlot-class.Rd
ChromHeatMap/man/ChrStrandData-class.Rd
ChromHeatMap/man/ChrStrandMatrix-class.Rd
ChromHeatMap/man/chrHeatMap.Rd
ChromHeatMap/man/chrNames.Rd
ChromHeatMap/man/chrdata.Rd
ChromHeatMap/man/createChrMatrix.Rd
ChromHeatMap/man/cytobands.Rd
ChromHeatMap/man/drawMapDendro.Rd
ChromHeatMap/man/grabChrMapProbes.Rd
ChromHeatMap/man/makeChrStrandData-methods.Rd
ChromHeatMap/man/makeChrStrandData.Rd
ChromHeatMap/man/makeRangedDataList.Rd
ChromHeatMap/man/plotChrMap.Rd
ChromHeatMap/man/stains.Rd
ChromHeatMap/man/strandName.Rd
ChromHeatMap/vignettes
ChromHeatMap/vignettes/ChromHeatMap.Rnw