vGWAS: Variance Genome-wide Association

In kullrich/vGWAS: Variance Heterogeneity Genome-wide Association Study - Reimplementation

Variance Genome-wide Association

Description

Variance Genome-wide association for using nonparametric variance test

Usage

vGWAS(phenotype, geno.matrix, kruskal.test = FALSE,
marker.map = NULL, chr.index = NULL, pB = TRUE)

Arguments

phenotype	a numeric or logical vector of the phenotyic values. See Examples.
geno.matrix	a matrix or data.frame with individuals as rows and markers as columns. The marker genotypes for each marker are coded as one column. See Examples.
kruskal.test	a logical value specifying whether to use Kruskal-Wallis statistic. The default option is FALSE, i.e., the usual ANOVA statistic is used in place of Kruskal-Wallis statistic.
marker.map	a numeric vector giving the marker map positions for each chromosome. See Examples.
chr.index	a numeric vector giving the chromosome index for each marker. See Examples.
pB	show progress bar

Value

a data.frame containing columns of marker names, chromosome indices, marker.map positions, test statistic values, and p.value for each position.

Author(s)

Xia Shen

References

Shen, X., Pettersson, M., Ronnegard, L. and Carlborg, O. (2011): Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. PLoS Genetics, 8, e1002839.

Ronnegard, L., Shen, X. and Alam, M. (2010): hglm: A Package for Fitting Hierarchical Generalized Linear Models. The R Journal, 2(2), 20-28.

See Also

package-vGWAS

Examples

# ----- load data ----- #
data(pheno)
data(geno)
data(chr)
data(map)
# ----- variance GWA scan ----- #
vgwa <- vGWAS(phenotype = pheno, geno.matrix = geno,
marker.map = map, chr.index = chr, pB = FALSE)
# ----- visualize the scan ----- #
plot(vgwa)
summary(vgwa)
# ----- calculate the variance explained by the strongest marker ----- #
vGWAS.variance(phenotype = pheno,
marker.genotype = geno[, vgwa[["p.value"]] == min(vgwa[["p.value"]])])
# ----- genomic control ----- #
vgwa2 <- vGWAS.gc(vgwa)
plot(vgwa2)
summary(vgwa2)

kullrich/vGWAS documentation built on June 10, 2025, 3:56 a.m.