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rNeighborQTL (version 1.1.1)

Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

Description

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. (2020) .

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Version

Install

install.packages('rNeighborQTL')

Monthly Downloads

680

Version

1.1.1

License

GPL-3

Maintainer

Yasuhiro Sato

Last Published

November 12th, 2020

Functions in rNeighborQTL (1.1.1)

min_dist

Calculating the minimum distance
sim_nei_qtl

Phenotype simulation for neighbor QTL effects
decompose_genoprobs

Decomposition of conditional genotype probabilities
eff_neighbor

Estimation of self and neighbor QTL effects across a genome
genoprobs2selfprobs

Calculating a set of self QTL effects from conditional genotype probabilities
get_markers

Reshaping marker information
scan_neighbor

Genome scan for neighbor effects with a QTL model
calc_pve

Calculating phenotypic variation explained by neighbor effects
calc_neiprob

Calculating a set of neighbor QTL effects from conditional genotype probabilities
plot_nei

Plot LOD score for self or neighbor QTL effects
int_neighbor

Testing marker-by-marker epistasis in neighbor QTL effects
logLik_glm.fit

Calculating log-likelihood in generalized linear models
selfprob

Calculating self QTL effects
rNeighborQTL-package

rNeighbor QTL: quantitative trait loci mapping for neighbor effects
perm_neighbor

Permutation tests for neighbor effects with a QTL model
plot_eff

Plot self and neighbor QTL effects across a genome
neiprob

Calculating neighbor QTL effects