calc_pve {rNeighborQTL} | R Documentation |
Calculating phenotypic variation explained by neighbor effects
Description
A function to calculate the proportion or ratio of phenotypic variation explained (PVE or RVE) by neighbor effects for a series of neighbor distance (s_seq
) using mixed models.
Usage
calc_pve(
genoprobs,
pheno,
smap,
s_seq,
addcovar = NULL,
grouping = rep(1, nrow(smap)),
response = c("quantitative", "binary"),
fig = TRUE,
contrasts = NULL
)
Arguments
genoprobs |
Conditional genotype probabilities as taken from |
pheno |
A vector of individual phenotypes. |
smap |
A matrix showing a spatial map for individuals. The first and second column include spatial positions along an x-axis and y-axis, respectively. |
s_seq |
A numeric vector including a set of the maximum spatial distance between a focal individual and neighbors to define neighbor effects. A scalar is also allowed. |
addcovar |
An optional matrix including additional non-genetic covariates. It contains no. of individuals x no. of covariates. |
grouping |
An optional integer vector assigning each individual to a group. This argument can be used when |
response |
An optional argument to select trait types. The |
fig |
TRUE/FALSE to add a figure of Delta PVE or not. |
contrasts |
An optional vector composed of three TRUE/FALSE values, which represents the presence/absence of specific genotypes as c(TRUE/FALSE, TRUE/FALSE, TRUE/FALSE) = AA, AB, BB. If |
Details
This function calls linear or logistic mixed models via the gaston
package (Perdry & Dandine-Roulland 2020).
If "quantitative"
is selected, Var_self
or Var_nei
in the output is given by the proportion of phenotypic variation explained (PVE) by neighbor effects as PVEnei =\sigma^2_2/(\sigma^2_1+\sigma^2_2+\sigma^2_e)
.
If "binary"
is selected, Var_self
or Var_nei
is given by the ratio of phenotypic variation explained (RVE) by neighbor effects as RVEnei =\sigma^2_2/\sigma^2_1
and p-values are not available.
This is because a logistic mixed model logistic.mm.aireml()
called via the gaston
package does not provide \sigma^2_e
and log-likelihood (see Chen et al. 2016 for the theory).
Value
A matrix containing the maximum neighbor distance, phenotypic variation explained by neighbor effects, and p-value by a likelihood ratio test.
scale
Maximum neighbor distance given as an argumentVar_self
Proportion or ratio of phenotypic variation explained (PVE or RVE) by self-genotype effects for linear or logistic mixed models, respectivelyVar_nei
Proportion or ratio of phenotypic variation explained (PVE or RVE) by neighbor effects for linear or logistic mixed models, respectivelyp-value
p-value by a likelihood ratio test between models with or without neighbor effects. Self effects are tested when the scale is zero
Author(s)
Yasuhiro Sato (sato.yasuhiro.36c@kyoto-u.jp)
References
Perdry H, Dandine-Roulland C (2020) gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models. R package version 1.5.6. https://CRAN.R-project.org/package=gaston
Chen H, Wang C, Conomos M. et al. (2016) Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models. The American Journal of Human Genetics 98: 653-666.
Examples
set.seed(1234)
test_map <- qtl::sim.map(len=rep(20,5),n.mar=3,include.x=FALSE)
test_cross <- qtl::sim.cross(test_map,n.ind=50)
test_smap <- cbind(runif(50,1,100),runif(50,1,100))
test_genoprobs <- qtl::calc.genoprob(test_cross,step=2)
s_seq <- quantile(dist(test_smap),c(0.1*(1:10)))
test_pve <- calc_pve(genoprobs=test_genoprobs,
pheno=test_cross$pheno$phenotype,
smap=test_smap, s_seq=s_seq,
)