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LDheatmap (version 0.99-7)

Graphical Display of Pairwise Linkage Disequilibria Between SNPs

Description

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. Users should note that the imported package 'snpStats' and the suggested packages 'rtracklayer', 'GenomicRanges', 'GenomInfoDb' and 'IRanges' are all BioConductor packages .

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Version

Install

install.packages('LDheatmap')

Monthly Downloads

231

Version

0.99-7

License

GPL-3

Maintainer

Brad McNeney

Last Published

July 14th, 2019

Functions in LDheatmap (0.99-7)

LDheatmap

This function produces a pairwise LD plot.
LDheatmap.addGrob

Add a graphical object to an LDheatmap plot
CHBJPTData

Example of data set for LDHeatmap
LDheatmap.addGenes

Add gene plot to an LDheatmap object.
GIMAP5

Example data set for LDHeatmap
LDheatmap-internal

Internal LDheatmap functions and data files
LDheatmap.addRecombRate

Add recombination rate plot to an LD heat map.
CEUData

Example data set for LDheatmap
LDheatmap.addScatterplot

Add a scatter plot to an LDheatmap object
GIMAP5.CEU

Example data set for LDheatmap
LDheatmap.highlight

Highlight a genetic region in the linkage disequilibrium heat map
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.
vcfR2SnpMatrix

Extract genotype information from a vcfR object