volcano_ic {biotmle}R Documentation

Volcano plot for class biotmle

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, fc_bound = 3, pval_bound = 0.2)

Arguments

biotmle

object of class biotmle as produced by an appropriate call to biomarkertmle

fc_bound

(numeric) - indicates the highest magnitude of the fold to be colored along 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

(numeric) - indicates the largest corrected p-value to be colored along 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

library(dplyr)
library(biotmleData)
library(SummarizedExperiment)
data(biomarkertmleOut)

limmaTMLEout <- modtest_ic(biotmle = biomarkerTMLEout)

volcano_ic(biotmle = limmaTMLEout)
#

[Package biotmle version 1.8.0 Index]