rNeighborGWAS: Testing Neighbor Effects in Marker-Based Regressions

Package: rNeighborGWAS 1.2.5

Yasuhiro Sato

rNeighborGWAS: Testing Neighbor Effects in Marker-Based Regressions

To incorporate neighbor genotypic identity into genome-wide association studies, the package provides a set of functions for variation partitioning and association mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1038/s41437-020-00401-w>.

Authors:Yasuhiro Sato [aut, cre], Eiji Yamamoto [aut], Kentaro K. Shimizu [aut], Atsushi J. Nagano [aut]

rNeighborGWAS_1.2.5.tar.gz
rNeighborGWAS_1.2.5.tar.gz(r-4.7-any)rNeighborGWAS_1.2.5.tar.gz(r-4.6-any)
rNeighborGWAS_1.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rNeighborGWAS/json (API)

# Install 'rNeighborGWAS' in R:

install.packages('rNeighborGWAS', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.51 score 16 scripts 513 downloads 2 mentions 9 exports 6 dependencies

Last updated from:9ee528022c. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	176
source / vignettes	OK	198
linux-release-x86_64	OK	170
wasm-release	OK	107

Exports:calc_PVEnei delta_PVE gaston2neiGWAS min_dist nei_coval nei_lm nei_lmm nei_simu neiGWAS

Dependencies:gaston lattice Matrix Rcpp RcppEigen RcppParallel

rNeighborGWAS

Rendered fromrNeighborGWAS.Rmdusingknitr::rmarkdown

Help page	Topics
Calculating phenotypic variation explained by neighbor effects	calc_PVEnei
Estimating the effective scale of neighbor effects	delta_PVE
Convert 'gaston' package's bed.matrix data to rNeighborGWAS genotype data.	gaston2neiGWAS
Calculating the minimum distance	min_dist
Calculating neighbor genotypic identity	nei_coval
Standard linear models for testing self and neighbor effects	nei_lm
Mixed models for testing self and neighbor effects	nei_lmm
Simulating phenotypes with self and neighbor effects	nei_simu
Genome-wide association mapping of neighbor effects	neiGWAS
Simulating phenotype values with neighbor effects.	qtl_pheno_simu
Calculating a distance decay weight	w

Help page

Topics

Calculating phenotypic variation explained by neighbor effects

calc_PVEnei

Estimating the effective scale of neighbor effects

delta_PVE

Convert 'gaston' package's bed.matrix data to rNeighborGWAS genotype data.

gaston2neiGWAS

Calculating the minimum distance

min_dist

Calculating neighbor genotypic identity

nei_coval