LDheatmap v1.0-4

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Graphical Display of Pairwise Linkage Disequilibria Between SNPs

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) <doi:10.18637/jss.v016.c03>. Users should note that the imported package 'snpStats' and the suggested packages 'rtracklayer', 'GenomicRanges', 'GenomInfoDb' and 'IRanges' are all BioConductor packages <https://bioconductor.org>.

Functions in LDheatmap

Name Description
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.
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Vignettes of LDheatmap

Name
1KG_sample_info.csv
LDheatmap.Rnw
LDheatmap.bib
gTree.pdf
jsslogo.jpg
snp_id_dist.csv
snp_in_vcf.vcf
vcfOnLDheatmap.Rmd
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Details

Date 2020-10-03
License GPL-3
URL https://sfustatgen.github.io/LDheatmap/
Repository CRAN
Date/Publication 2020-10-08 10:00:02 UTC
RoxygenNote 7.1.0
LinkingTo Rcpp
NeedsCompilation yes
Packaged 2020-10-03 16:53:57 UTC; mcneney

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