% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/plots.R

\name{plot.bioTMLE}

\alias{plot.bioTMLE}

\title{Plot p-values from moderated statistical tests for class biotmle}

\usage{

\method{plot}{bioTMLE}(x, ..., type = "pvals_adj")

}

\arguments{

\item{x}{object of class \code{biotmle} as produced by an appropriate call

to \code{biomarkertmle}}

\item{...}{additional arguments passed \code{plot} as necessary}

\item{type}{character describing whether to provide a plot of unadjusted or

adjusted p-values (adjustment performed via Benjamini-Hochberg)}

}

\value{

object of class \code{ggplot} containing a histogram of the raw or

 Benjamini-Hochberg corrected p-values (depending on user input).

}

\description{

Histogram of raw or FDR-adjusted p-values from the moderated t-test.

}

\examples{

\dontrun{

library(dplyr)

library(biotmleData)

library(SuperLearner)

library(SummarizedExperiment)

data(illuminaData)

colData(illuminaData) <- colData(illuminaData) \%>\%

  data.frame() \%>\%

  mutate(age = as.numeric(age > median(age))) \%>\%

  DataFrame()

benz_idx <- which(names(colData(illuminaData)) \%in\% "benzene")

biomarkerTMLEout <- biomarkertmle(

  se = illuminaData,

  varInt = benz_idx,

  bppar_type = BiocParallel::SerialParam(),

  g_lib = c("SL.mean", "SL.glm"),

  Q_lib = c("SL.mean", "SL.glm")

)

limmaTMLEout <- modtest_ic(biotmle = biomarkerTMLEout)

plot(x = limmaTMLEout, type = "pvals_adj")

}

}