snp_gc: Genomic Control

In bigsnpr: Analysis of Massive SNP Arrays

Genomic Control

Description

Genomic Control

Usage

snp_gc(gwas)

Arguments

gwas	A mhtest object with the p-values associated with each SNP. Typically, the output of bigstatsr::big_univLinReg, bigstatsr::big_univLogReg or snp_pcadapt.

Value

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.

References

Devlin, B., & Roeder, K. (1999). Genomic control for association studies. Biometrics, 55(4), 997-1004.

Examples

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) # this modifies `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) +
  ggplot2::geom_hline(yintercept = -log10(5e-8), linetype = 2, color = "red")

p <- snp_qq(gwas_gc) +
  ggplot2::aes(text = asPlotlyText(test$map)) +
  ggplot2::labs(subtitle = NULL, x = "Expected -log10(p)", y = "Observed -log10(p)")
## Not run: plotly::ggplotly(p, tooltip = "text")

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.