Other packages > Find by keyword >

GenomeAdapt  

Detecting Signatures of Local Adaptation Based on Ancestry Trajectories
View on CRAN: Click here


Download and install GenomeAdapt package within the R console
Install from CRAN:
install.packages("GenomeAdapt")

Install from Github:
library("remotes")
install_github("cran/GenomeAdapt")

Install by package version:
library("remotes")
install_version("GenomeAdapt", "1.0.0")



Attach the package and use:
library("GenomeAdapt")
Maintained by
Xinghu Qin
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-11-11
Latest Update:
Description:
Portable, scalable and highly computationally efficient tool for detecting signatures of local adaptation based on multidimensional ancestry map ( _n_ X _n_ ancestry genetic trajectories, _n_ is the number of individuals). If n samples are included in the analysis, there will be n dimensional spaces that represent the common ancestry maps based on the identity-by-descent (IBD). The package calculates the correlations of loci with the common ancestry genetic maps adopting the Genomic Data Structure (GDS, Zheng et al., 2012) and suitable for millions of SNP data. Loci sharing a greater level of most recent common ancestor (MRCA) (large Z-scores) indicates a large number of individuals descend from recent common ancestors, which signals the rapid increase in frequency of a beneficial allele due to recent positive selection. The rationale underlying this package is somewhat analogous to KLFDAPT (Qin, 2021) (). It combines the concept of IBD-based genome scan (Albrechtsen et al., 2010) , iHS (Voight, 2006) , and eigenanalysis of SNP data with an identity by descent interpretation (Zheng & Weir, 2016) . It can also be interpreted as spatial varying selection as ancestry genetic maps reflect geographic origins. Besides the detection of local adaptation, this package also estimates the population admixtures and plots its geographic genetic structure.
How to cite:
Xinghu Qin (2021). GenomeAdapt: Detecting Signatures of Local Adaptation Based on Ancestry Trajectories. R package version 1.0.0, https://cran.r-project.org/web/packages/GenomeAdapt. Accessed 28 Jun. 2026.
Previous versions and publish date:
1.0.0 (2021-11-11 20:40)
Other packages that cited GenomeAdapt R package
View GenomeAdapt citation profile
Other R packages that GenomeAdapt depends, imports, suggests or enhances
Functions, R codes and Examples using the GenomeAdapt R package
Some associated functions: AdmixProp . GenomeAdapt . PlotAdmix . plotmanhattan . zscores_qvals . 
Some associated R codes: Ancestry_prop.R . GenomeAdapt.R . zscores.R .  Full GenomeAdapt package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
arnie  
"Arnie" box office records 1982-2014
Arnold Schwarzenegger movie weekend box office records from1982-2014 ...
Download / Learn more Package Citations See dependency  
Rirt  
Data Analysis and Parameter Estimation Using Item Response Theory
Parameter estimation, computation of probability, information, and (log-)likelihood, and visualizat ...
Download / Learn more Package Citations See dependency  
EventWinRatios  
Event-Specific Win Ratios for Terminal and Non-Terminal Events
Provides several confidence interval and testing procedures using event-specific win ratios for sem ...
Download / Learn more Package Citations See dependency  
nlraa  
Nonlinear Regression for Agricultural Applications
Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is ...
Download / Learn more Package Citations See dependency  
XKCDdata  
Get XKCD Comic Data
Download data from individual XKCD comics, written by Randall Munroe < ...
Download / Learn more Package Citations See dependency  

27,653

R Packages

236,180

Dependencies

73,487

Author Associations

27,536

Publication Badges

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