plot_qq: Generate qq plots from p values

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Generate qq plots from p values

Description

Generate qq (quantile-quantile) plots for p-values, splitting by provided facets, using either a snpRdata object or a data.frame. Produces a ggplot object, which is modifiable as usual.

Usage

plot_qq(x, plot_var, facets = NULL, lambda_gc_correction = FALSE)

Arguments

x	snpRdata object or data.frame containing p-values to plot.
plot_var	character, name of the p-values to plot. For a snpRdata object, the name should refer to the name of the column produced when fetching data via get.snpR.stats. For a data.frame, it should refer to the column name directly.
facets	character, default NULL. Facets by which to split the plot. See Facets_in_snpR.
lambda_gc_correction	Correct for inflated significance due to population and/or family structure using the \gamma_{GC} approach described in Price et al 2010.

Author(s)

William Hemstrom

References

Price, A., Zaitlen, N., Reich, D. et al. New approaches to population stratification in genome-wide association studies. Nat Rev Genet 11, 459–463 (2010). https://doi.org/10.1038/nrg2813

Examples

## Not run: 
# from a snpRdata object directly
x <- stickSNPs
sample.meta(x)$phenotype <- sample(c("case", "control"), nsamps(stickSNPs), TRUE)
x <- calc_association(x, c("pop.fam", "pop", ".base"), "phenotype",
                      method = "armitage")
p <- plot_qq(x, "p_armitage_phenotype", c("pop.fam", "pop", ".base"))
                      
                      
# from a data.frame
y <- get.snpR.stats(x, c("pop.fam", "pop", ".base"), "association")
y <- y$single


# with facet/subfacet columns:
p <- plot_qq(y, "p_armitage_phenotype", c("fam.pop", "pop", ".base"))


# from raw data with only one faceting column
z <- y[y$facet == "pop",]
z <- z[,c(1, 5)]
colnames(z)[1] <- "pop"
p <- plot_qq(z, "p_armitage_phenotype", "pop")

## End(Not run)

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.