dive_phe2mash function v1 to test on several plant species

man/get_qqplot.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/wrapper.R
+\name{get_qqplot}
+\alias{get_qqplot}
+\title{Create a quantile-quantile plot with ggplot2.}
+\usage{
+get_qqplot(ps, ci = 0.95, lambdaGC = FALSE, tol = 1e-08)
+}
+\arguments{
+\item{ps}{Numeric vector of p-values.}
+
+\item{ci}{Numeric. Size of the confidence interval, 0.95 by default.}
+
+\item{lambdaGC}{Logical. Add the Genomic Control coefficient as subtitle to
+the plot?}
+
+\item{tol}{Numeric. Tolerance for optional Genomic Control coefficient.}
+}
+\value{
+A ggplot2 plot.
+}
+\description{
+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.
+}