calc_neiprob {rNeighborQTL} | R Documentation |
Calculating a set of neighbor QTL effects from conditional genotype probabilities
Description
A function to calculate self QTL effects for all individuals, with given deviation coefficients and conditional genotype probabilities.
Usage
calc_neiprob(
genoprobs,
a2,
d2,
contrasts = NULL,
smap,
scale,
grouping = rep(1, nrow(smap)),
d2sq0 = FALSE
)
Arguments
genoprobs |
Conditional genotype probabilities as taken from |
a2 |
A numeric scalar indicating additive deviation. |
d2 |
A numeric scalar indicating dominance deviation. |
contrasts |
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. |
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. |
scale |
A numeric scalar indicating the maximum spatial distance between a focal individual and neighbors to define neighbor effects. |
grouping |
An integer vector assigning each individual to a group. This argument can be used when |
d2sq0 |
An option to make AB/AB interaction effects zero. |
Value
A numeric matrix containing individuals x marker elements for neighbor QTL effects.
Author(s)
Yasuhiro Sato (sato.yasuhiro.36c@kyoto-u.jp)