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LDheatmap (version 1.0-4)

Graphical Display of Pairwise Linkage Disequilibria Between SNPs

Description

Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between single nucleotide polymorphisms (SNPs). Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The methods are described in Shin et al. (2006) . 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

1.0-4

License

GPL-3

Maintainer

Brad McNeney

Last Published

October 8th, 2020

Functions in LDheatmap (1.0-4)

CHBJPTData

Example of data set for LDHeatmap
GIMAP5.CEU

Example data set for LDheatmap
LDheatmap.addGrob

Add a graphical object to an LDheatmap plot
LDheatmap-internal

Internal LDheatmap functions and data files
GIMAP5

Example data set for LDHeatmap
CEUData

Example data set for LDheatmap
LDheatmap.addGenes

Add gene plot to an LDheatmap object.
LDheatmap.addScatterplot

Add a scatter plot to an LDheatmap object
LDheatmap

This function produces a pairwise LD plot.
LDheatmap.addRecombRate

Add recombination rate plot to an LD heat map.
plotGenes

Plot genes from a specified region of the human genome.
LDheatmap.highlight

Highlight a genetic region in the linkage disequilibrium heat map
vcfR2SnpMatrix

Extract genotype information from a vcfR object
LDheatmap.marks

Plots a symbol in the centers of cells of the heat map image
recombRate

Produce recombination rate plot.