calc_neiprob {rNeighborQTL}

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 qtl::calc.genoprob().

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 smap contains different experimental replicates. Default setting means that all individuals are belong to a single group.

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 ([e-mail])