LDheatmap: Graphical Display of Pairwise Linkage Disequilibria Between SNPs

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Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot.

Author
Ji-Hyung Shin <shin@sfu.ca>, Sigal Blay <sblay@sfu.ca>, Nicholas Lewin-Koh <nikko@hailmail.net>, Brad McNeney <mcneney@sfu.ca>, Jinko Graham <jgraham@sfu.ca>
Date of publication
2016-08-24 18:02:24
Maintainer
Brad McNeney <mcneney@sfu.ca>
License
GPL-3
Version
0.99-2
URLs

View on CRAN

Man pages

CEUData
Example data set for LDheatmap
CHBJPTData
Example data set for LDheatmap
GIMAP5
Example data set for LDheatmap
GIMAP5CEU
Example data set for LDheatmap
LDheatmap
This function produces a pairwise LD plot.
LDheatmap.addGenes
Add gene plot to an LDheatmap object.
LDheatmap.addGrob
Add a graphical object to an LDheatmap plot
LDheatmap.addRecombRate
Add recombination rate plot to an LD heat map.
LDheatmap.addScatterplot
Add a scatter plot to an LDheatmap object
LDheatmap.highlight
Highlight a genetic region in the linkage disequilibrium heat...
LDheatmap-internal
Internal LDheatmap functions and data files
LDheatmap.marks
Plots a symbol in the centers of cells of the heat map image
plotGenes
Plot genes from a specified region of the human genome.
recombRate
Produce recombination rate plot.

Files in this package

LDheatmap
LDheatmap/inst
LDheatmap/inst/CITATION
LDheatmap/inst/ChangeLog
LDheatmap/inst/extdata
LDheatmap/inst/extdata/addTracks.RData
LDheatmap/inst/doc
LDheatmap/inst/doc/LDheatmap.pdf
LDheatmap/inst/doc/LDheatmap.R
LDheatmap/inst/doc/addTracks.Rnw
LDheatmap/inst/doc/addTracks.R
LDheatmap/inst/doc/addTracks.pdf
LDheatmap/inst/doc/LDheatmap.Rnw
LDheatmap/NAMESPACE
LDheatmap/demo
LDheatmap/demo/LDheatmap.R
LDheatmap/demo/00Index
LDheatmap/data
LDheatmap/data/CHBJPTData.rda
LDheatmap/data/GIMAP5.RData
LDheatmap/data/hapmapCHB.txt.gz
LDheatmap/data/hapmapCEU.txt.gz
LDheatmap/data/hapmapJPT.txt.gz
LDheatmap/data/datalist
LDheatmap/data/CEUData.rda
LDheatmap/data/GIMAP5.CEU.RData
LDheatmap/R
LDheatmap/R/utils.R
LDheatmap/R/LDheatmap.marks.R
LDheatmap/R/LDheatmap.highlight.R
LDheatmap/R/LDheatmap.R
LDheatmap/R/LDheatmap.addGenes.R
LDheatmap/R/plotGenes.R
LDheatmap/R/LDheatmap.addRecombRate.R
LDheatmap/R/LDheatmap.addScatterplot.R
LDheatmap/R/LDheatmap.addGrob.R
LDheatmap/R/recombRate.R
LDheatmap/vignettes
LDheatmap/vignettes/LDheatmap.bib
LDheatmap/vignettes/addTracks.Rnw
LDheatmap/vignettes/gTree.pdf
LDheatmap/vignettes/LDheatmap.Rnw
LDheatmap/vignettes/jsslogo.jpg
LDheatmap/MD5
LDheatmap/build
LDheatmap/build/vignette.rds
LDheatmap/DESCRIPTION
LDheatmap/man
LDheatmap/man/GIMAP5.Rd
LDheatmap/man/CHBJPTData.Rd
LDheatmap/man/LDheatmap.highlight.Rd
LDheatmap/man/recombRate.Rd
LDheatmap/man/LDheatmap-internal.Rd
LDheatmap/man/GIMAP5CEU.Rd
LDheatmap/man/CEUData.Rd
LDheatmap/man/LDheatmap.marks.Rd
LDheatmap/man/LDheatmap.Rd
LDheatmap/man/LDheatmap.addGenes.Rd
LDheatmap/man/LDheatmap.addGrob.Rd
LDheatmap/man/LDheatmap.addScatterplot.Rd
LDheatmap/man/LDheatmap.addRecombRate.Rd
LDheatmap/man/plotGenes.Rd