LDheatmap v0.99-7
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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 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 <https://bioconductor.org>.
Functions in LDheatmap
| Name | Description | |
| 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 | |
| No Results! | ||
Vignettes of LDheatmap
| Name | ||
| 1KG_sample_info.csv | ||
| LDheatmap.Rnw | ||
| LDheatmap.bib | ||
| addTracks.Rnw | ||
| gTree.pdf | ||
| jsslogo.jpg | ||
| snp_id_dist.csv | ||
| snp_in_vcf.vcf | ||
| vcfOnLDheatmap.Rmd | ||
| No Results! | ||
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Details
| Date | 2019-07-01 |
| License | GPL-3 |
| URL | https://sfustatgen.github.io/LDheatmap/ |
| Repository | CRAN |
| Date/Publication | 2019-07-14 22:10:40 UTC |
| RoxygenNote | 6.1.1 |
| LinkingTo | Rcpp |
| NeedsCompilation | yes |
| Packaged | 2019-07-13 18:11:25 UTC; mcneney |
| imports | genetics , grid , Rcpp , snpStats |
| suggests | GenomeInfoDb , GenomicRanges , ggplot2 , IRanges , lattice , rtracklayer , vcfR |
| depends | R (>= 2.14.0) |
| Contributors | S Blay, Nicholas LewinKoh, Ji-Hyung Shin, Jinko Graham, Gloria Yang, Matthew Reyers, Youwei Yan |
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