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In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
snplinkage-package R Documentation
snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
Description
Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.13097/archive-ouverte/unige:161795")}.
Author(s)
Maintainer: Thomas Charlon charlon@protonmail.com (ORCID)
Authors:
Karl Forner
Alessandro Di Cara
Jérôme Wojcik
See Also
Useful links:
snplinkage documentation built on Sept. 11, 2024, 6:02 p.m.
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| snplinkage-package | R Documentation |
snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
Description
Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.13097/archive-ouverte/unige:161795")}.
Author(s)
Maintainer: Thomas Charlon charlon@protonmail.com (ORCID)
Authors:
Karl Forner
Alessandro Di Cara
Jérôme Wojcik
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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