Variance GWA Summary

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Description

The function summarized the variance GWA result for the given scan object.

Usage

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## S3 method for class 'vGWAS'
summary(object, nrMarkers = 10, ...)

Arguments

object

a result object from vGWAS scan. It can be any list or data.frame that contains chromosome, marker.map, and p.value, with class = 'vGWAS'. See vGWAS.

nrMarkers

a numeric value giving the number of top markers to be summarized.

...

Not in use.

Value

a summary for viewing vGWAS result.

Author(s)

Simon Forsberg, 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

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## 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)