Other packages > Find by keyword >

snplinkage  

Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
View on CRAN: Click here


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", "1.2.0")



Attach the package and use:
library("snplinkage")
Maintained by
Thomas Charlon
[Scholar Profile | Author Map]
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 1.2.0, https://cran.r-project.org/web/packages/snplinkage. Accessed 29 Mar. 2025.
Previous versions and publish date:
1.0.0 (2023-05-04 10:10)
Other packages that cited snplinkage R package
View snplinkage citation profile
Other R packages that snplinkage depends, imports, suggests or enhances
Complete documentation for snplinkage
Downloads during the last 30 days
02/2702/2803/0103/0203/0303/0403/0503/0603/0703/0803/0903/1003/1103/1203/1303/1403/1503/1603/1703/1803/1903/2003/2103/2203/2303/2403/2503/2603/27Downloads for snplinkage4681012141618TrendBars

Today's Hot Picks in Authors and Packages

landmix  
Landmark Prediction for Mixture Data
Non-parametric prediction of survival outcomes for mixture data that incorporates covariates and a l ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
gglgbtq  
Show Pride on 'ggplot2' Plots
Provides multiple palettes based on pride flags with tailored themes. ...
Download / Learn more Package Citations See dependency  

23,842

R Packages

207,311

Dependencies

64,420

Author Associations

23,781

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA