volcano_ic: Volcano plot for class biotmle

In nhejazi/biotmle: Targeted Learning with Moderated Statistics for Biomarker Discovery

Description

Volcano plot of the log-changes in the target causal paramter against the log raw p-values from the moderated t-test.

Usage

volcano_ic(biotmle, ate_bound = 1, pval_bound = 0.2)

Arguments

biotmle	object of class biotmle as produced by an appropriate call to biomarkertmle
ate_bound	A numeric indicating the highest magnitude of the average treatment effect to be colored on the x-axis of the volcano plot; this limits the observations to be considered differentially expressed to those in a user-specified interval.
pval_bound	A numeric indicating the largest corrected p-value to be colored on the y-axis of the volcano plot; this limits observations considered as differentially expressed to those in a user-specified interval.

Value

object of class ggplot containing a standard volcano plot of the log-fold change in the causal target parameter against the raw log p-value computed from the moderated tests in modtest_ic.

Examples

## Not run: 
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)

volcano_ic(biotmle = limmaTMLEout)

## End(Not run)

nhejazi/biotmle documentation built on Oct. 15, 2021, 5:46 p.m.