Genomic Control
Genomic Control
snp_gc(gwas)
gwas |
A |
A ggplot2 object. You can plot it using the print method.
You can modify it as you wish by adding layers. You might want to read
this chapter
to get more familiar with the package ggplot2.
Devlin, B., & Roeder, K. (1999). Genomic control for association studies. Biometrics, 55(4), 997-1004.
set.seed(9)
test <- snp_attachExtdata()
G <- test$genotypes
y <- rnorm(nrow(G))
gwas <- big_univLinReg(G, y)
snp_qq(gwas)
gwas_gc <- snp_gc(gwas) # change attr(gwas_gc, "transfo")
snp_qq(gwas_gc)
# The next plot should be prettier with a real dataset
snp_manhattan(gwas_gc,
infos.chr = test$map$chromosome,
infos.pos = test$map$physical.pos)
p <- snp_qq(gwas_gc) + ggplot2::aes(text = asPlotlyText(test$map))
## Not run: plotly::ggplotly(p, tooltip = "text")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.