pvdiv_qqplot: Create a quantile-quantile plot with ggplot2.
In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum

Assumptions for this quantile quantile plot: Expected P values are uniformly distributed. Confidence intervals assume independence between tests. We expect deviations past the confidence intervals if the tests are not independent. For example, in a genome-wide association study, the genotype at any position is correlated to nearby positions. Tests of nearby genotypes will result in similar test statistics.

pvdiv_qqplot(
  ps,
  effects = NULL,
  ind = NULL,
  ci = 0.95,
  lambdaGC = FALSE,
  tol = 1e-08
)

`ps`	Numeric vector of p-values.
`effects`	a gwas effects FBM object created using 'pvdiv_standard_gwas'. Saved under the name "gwas_effects_suffix.rds" and can be loaded into R using the bigstatsr function "big_attach".
`ind`	If effects is a FBM object, this should be the row number of the phenotype from the associated metadata for the FBM object.
`ci`	Numeric. Size of the confidence interval, 0.95 by default.
`lambdaGC`	Logical. Add the Genomic Control coefficient as subtitle to the plot?
`tol`	Numeric. Tolerance for optional Genomic Control coefficient.