Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/scan_neighbor.R
Genome scan using a QTL model for self and neighbor effects, with possible allowance for additional covariates and non-normal traits. Theoretical background is described in Sato, Takeda & Nagano (2021).
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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. |
scale |
A numeric scalar indicating the maximum spatial distance between a focal individual and neighbors to define neighbor effects. |
addcovar |
An optional matrix including additional non-genetic covariates. It contains no. of individuals x no. of covariates. |
addQTL |
An optional vector containing marker names that are considered covariates. Namely, this option allows composite interval mapping (Jansen 1993). |
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 |
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 |
This function calculates LOD score after the additive and dominance deviation are estimated using eff_neighbor()
.
As it adopts a stepwise testing from self to neighbor effects, LOD_self
are the same as standard QTL mapping.
Note that the results return 0 LOD scores for covariate markers when using addQTL
option.
A matrix of LOD scores for self and neighbor effects, with the chromosome numbers and positions. The row names correspond to marker names.
chr
Chromosome number
pos
Marker position
LOD_self
LOD score for self effects
LOD_nei
LOD score for neighbor effects
Yasuhiro Sato (sato.yasuhiro.36c@kyoto-u.jp)
Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205-211.
Sato Y, Takeda K, Nagano AJ (2021) Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects. G3; Genes|Genomes|Genetics 11:jkab017.
1 2 3 4 5 6 7 8 9 10 11 | 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)
test_scan <- scan_neighbor(genoprobs=test_genoprobs,
pheno=test_cross$pheno$phenotype,
smap=test_smap, scale=20
)
plot_nei(test_scan)
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