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snplinkage
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Download and install snplinkage package within the R console
Install from CRAN:
install.packages("snplinkage")
Install from Github:
library("remotes")
install_github("cran/snplinkage")
Install by package version:
library("remotes")
install_version("snplinkage", "1.0.0")
Attach the package and use:
library("snplinkage")
Maintained by
Thomas Charlon
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-05-04
Latest Update: 2023-05-04
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) <doi:10.13097/archive-ouverte/unige:161795>.
How to cite:
Thomas Charlon (2023). snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations. R package version 1.0.0, https://cran.r-project.org/web/packages/snplinkage
Previous versions and publish date:
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Functions, R codes and Examples using
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Some associated functions: chisq_pvalues . chisq_pvalues_gdata . compound . diamond_annots . exposition . gdata_add_gene_annots . gdata_add_gene_annots_aim_example . gdata_add_gene_annots_hladr_example . gdata_scans_annots . gdata_snps_annots . get_biomart_metadb . ggplot_associations . ggplot_ld . ggplot_snp_pos . gtable_ld . gtable_ld_associations . gtable_ld_associations_gdata . gtable_ld_gdata . load_gds_as_genotype_data . parallel_apply . pipe . print_qc_as_tex_table . save_hgdp_as_gds . select_region_idxs . snplinkage-package . snprelate_allele_frequencies . snprelate_ld . snprelate_ld_select . snprelate_qc .
Some associated R codes: 0_imports.R . 1_allclasses.R . 2_all_generics.R . 4_methods.R . 5_methods_genotype_data_subset.R . associations.R . biomart_annots.R . fetch_hgdp.R . geno_data_convert.R . geno_data_fetch.R . ggplots_ld.R . gtable_associations.R . gtable_ld.R . snplinkage-package.R . snprelate_ld.R . snprelate_qc.R . utils.R . Full snplinkage package functions and examples
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