vGWAS.gc: Genomic Control for vGWAS

In vGWAS: Variance Heterogeneity Genome-Wide Association Study

Description

The function does genomic control for the variance GWA result object.

Usage

vGWAS.gc(object, plot = TRUE, proportion = 1, ...)

Arguments

object	a result object from vGWAS scan. It can be any list or data.frame that contains p.value. See vGWAS.
plot	a logical value turning on/off the QQ plot for genomic control.
proportion	a numeric value between 0 and 1 giving the proportion of obtained p-values to be used for genomic control.
...	not used.

Value

lambda	estimated inflation ratio.
lambda.se	standard error of the estimated inflation ratio.
gc.p.value	p-values after genomic control.

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. Submitted.

See Also

vGWAS-package, vGWAS

Examples

## Not run: 

# ----- 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)
              
# ----- visualize the scan ----- #

plot(vgwa)

summary(vgwa)

# ----- calculate the variance explained by strongest the marker ----- #

vGWAS.heritability(phenotype = pheno, 
                   marker.genotype = geno[,vgwa$p.value == min(vgwa$p.value)])
                   
# ----- genomic control ----- #

vgwa2 <- vGWAS.gc(vgwa)
                                
plot(vgwa2) 

summary(vgwa2)

## End(Not run)

vGWAS documentation built on May 2, 2019, 6:48 p.m.