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. | |
| No Results! | ||
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 | ||
| No Results! | ||
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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 |
| imports | genetics , grid , Rcpp , snpStats |
| suggests | GenomeInfoDb , GenomicRanges , ggplot2 , IRanges , lattice , rtracklayer , vcfR |
| depends | R (>= 4.0) |
| Contributors | S Blay, Nicholas LewinKoh, Ji-Hyung Shin, Jinko Graham, Gloria Yang, Matthew Reyers, Youwei Yan |
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