lmem.gwaser (version 0.1.0)

linkdis.plots: Linkage Disequilibrium heatmap plot

Description

Performs a Linkage Disequilibrium heatmap plot for the GWAS analysis. Non-random association of markers (linkage disequilibrium) are estimated as Lewont in $'/c$s $D'/c$ (Lewontin$'/c$s, 1964) with the LD function of the genetics package (Warnes and Leisch, 2005) and isualized with the LD.heatmap package (Shin et al., 2015). $D'/c$ is estimated as: $D'/c = D/DMax$ where D= pAB - pApB, DMax=Min (pApb, papB), and pA is the probability of the A allele for marker 1, pa=1-pA, pB is the probability of the B allele for marker 2, pb=1-pB, and pAB is the probability of AB alleles.

Usage

linkdis.plots (crossobj, heterozygotes, chr)

Arguments

crossobj

An object of class = cross obtained from the gwas.cross function from this package, or the read.cross function from r/qtl package (Broman and Sen, 2009). This file contains phenotypic means, genotypic marker score, and genetic map.

heterozygotes

Logical value indicating whether heterozygotes are present.

chr

A vector containing chromosome number to use.

Value

Return a Linkage Disequilibrium heatmap plot.

Details

The function returns the LD.heatmap for the chromosomes selected.

References

Comadran J, Thomas W, van Eeuwijk F, Ceccarelli S, Grando S, Stanca A, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett C, Russell J (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119:175-187

Warnes, G; Leisch, F. 2005. Genetics: Population genetics R package 1.2.0. Lewontin, R. 1964. The interaction of selection and linkage. I. General Considerations: Heterotic models. Genetics 49: 49-67.

See Also

gwas.analysis

Examples

## Not run: 
# data (QA_geno)
# data (QA_map)
# data (QA_pheno)
# 
# P.data <- QA_pheno
# G.data <- QA_geno
# map.data <- QA_map
# 
# cross.data <- gwas.cross (P.data, G.data, map.data,
# cross='gwas', heterozygotes=FALSE)
# summary (cross.data)
# 
# LD.plots
# 
# linkdis.plots(crossobj = cross.data, heterozygotes = FALSE, chr = c('1', '7'))
# ## End(Not run)