
A function to calculate self QTL effects for all individuals, with given deviation coefficients and conditional genotype probabilities.
calc_neiprob(
genoprobs,
a2,
d2,
contrasts = NULL,
smap,
scale,
grouping = rep(1, nrow(smap)),
d2sq0 = FALSE
)
Conditional genotype probabilities as taken from qtl::calc.genoprob()
.
A numeric scalar indicating additive deviation.
A numeric scalar indicating dominance deviation.
A 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.
A matrix showing a spatial map for individuals. The first and second column include spatial positions along an x-axis and y-axis, respectively.
A numeric scalar indicating the maximum spatial distance between a focal individual and neighbors to define neighbor effects.
An integer vector assigning each individual to a group. This argument can be used when smap
contains different experimental replicates. Default setting means that all individuals are belong to a single group.
An option to make AB/AB interaction effects zero.
A numeric matrix containing individuals x marker elements for neighbor QTL effects.