Description Usage Arguments Value Author(s) References See Also Examples
The function summarized the variance GWA result for the given scan object.
1 2 |
object |
a result object from |
nrMarkers |
a numeric value giving the number of top markers to be summarized. |
... |
Not in use. |
a summary for viewing vGWAS result.
Simon Forsberg, Xia Shen
Shen, X., Pettersson, M., Ronnegard, L. and Carlborg, O. (2011): Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana. Submitted.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ## 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)
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