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: 2023-12-02
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 21 Apr. 2025.
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
03/2403/2804/0104/0204/0504/0704/0804/0904/1204/1504/1704/18Downloads for GenomeAdapt123456789TrendBars

Today's Hot Picks in Authors and Packages

HellCor  
The Hellinger Correlation
Empirical value of the Hellinger correlation, a measure of dependence between two continuous random ...
Download / Learn more Package Citations See dependency  
discretecdAlgorithm  
Coordinate-Descent Algorithm for Learning Sparse Discrete Bayesian Networks
Structure learning of Bayesian network using coordinate-descent algorithm. This algorithm is design ...
Download / Learn more Package Citations See dependency  
bigsparser  
Sparse Matrix Format with Data on Disk
Provide a sparse matrix format with data stored on disk, to be used in both R and C++. This is inte ...
Download / Learn more Package Citations See dependency  
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  
bssn  
Birnbaum-Saunders Model
It provides the density, distribution function, quantile function, random number generator, reliabil ...
Download / Learn more Package Citations See dependency  

24,098

R Packages

207,311

Dependencies

65,069

Author Associations

24,099

Publication Badges

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