rNeighborQTL: Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

Package: rNeighborQTL 1.1.2

Yasuhiro Sato

rNeighborQTL: Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1093/g3journal/jkab017>.

Authors:Yasuhiro Sato [aut, cre], Kazuya Takeda [aut], Atsushi J. Nagano [aut]

rNeighborQTL_1.1.2.tar.gz
rNeighborQTL_1.1.2.tar.gz(r-4.7-any)rNeighborQTL_1.1.2.tar.gz(r-4.6-any)
rNeighborQTL_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rNeighborQTL/json (API)

# Install 'rNeighborQTL' in R:

install.packages('rNeighborQTL', 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.

2.00 score 4 scripts 748 downloads 1 mentions 8 exports 7 dependencies

Last updated from:7ccb50985b. Checks:2 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	139
source / vignettes	OK	205
linux-release-x86_64	NOTE	146
wasm-release	OK	108

Exports:calc_pve eff_neighbor int_neighbor min_dist perm_neighbor plot_nei scan_neighbor sim_nei_qtl

Dependencies:gaston lattice Matrix qtl Rcpp RcppEigen RcppParallel

rNeighborQTL

Rendered fromrNeighborQTL.Rmdusingknitr::rmarkdown

Help page	Topics
Calculating a set of neighbor QTL effects from conditional genotype probabilities	calc_neiprob
Calculating phenotypic variation explained by neighbor effects	calc_pve
Decomposition of conditional genotype probabilities	decompose_genoprobs
Estimation of self and neighbor QTL effects across a genome	eff_neighbor
Calculating a set of self QTL effects from conditional genotype probabilities	genoprobs2selfprobs
Reshaping marker information	get_markers
Testing marker-by-marker epistasis in neighbor QTL effects	int_neighbor
Calculating log-likelihood in generalized linear models	logLik_glm.fit
Calculating the minimum distance	min_dist
Calculating neighbor QTL effects	neiprob
Permutation tests for neighbor effects with a QTL model	perm_neighbor
Plot self and neighbor QTL effects across a genome	plot_eff
Plot LOD score for self or neighbor QTL effects	plot_nei
Genome scan for neighbor effects with a QTL model	scan_neighbor
Calculating self QTL effects	selfprob
Phenotype simulation for neighbor QTL effects	sim_nei_qtl

Help page

Topics

Calculating a set of neighbor QTL effects from conditional genotype probabilities

calc_neiprob

Calculating phenotypic variation explained by neighbor effects

calc_pve

Decomposition of conditional genotype probabilities

decompose_genoprobs

Estimation of self and neighbor QTL effects across a genome

eff_neighbor

Calculating a set of self QTL effects from conditional genotype probabilities

genoprobs2selfprobs