gClinBiomarker

Overview

gClinBiomarker is an R package that contains functions to perform baseline and longitutinal biomarker analyses

Two documents are provided: - A user vignette demonstrates how gClinBiomarker package may help in your biomarker analysis - An exapmle use case document which contains more detailed use cases

pdf version of these two documents can be found at inst/doc: https://github.com/lengning/gClinBiomarker/tree/master/inst/doc

The Rmarkdown templates to run the automatic workflows can be found here: https://github.com/lengning/gClinBiomarker-templates

Getting Started

Installation

To install this package from R, use install_github() function from the devtools package

In R, type:

## install.packages("devtools")
library(devtools)
install_github("lengning/gClinBiomarker")

Getting the Documentation

Use the command vignette(package = 'gClinBiomarker') to view a list of avaialble vignettes for the gClinBiomarker package. Then use the command vignette(<vignett_name>) to view the relevant documentation.

gClinBiomarker Analysis and Workflows

Supported endpoint and biomarker types

Endpoints

• Time-to-event
• Binary
• Continuous
• Longitudinal

Biomarkers

• Continuous
• Ordinal
• Categorical
• Longitudinal

Analysis

• 2-arm study: predictive and prognostic biomarker analysis
• 1-arm study: prognostic biomarker analysis

Workflow

Step 1:

Is your biomarker population your full patient population? Take a look at these functions:

SummaryVars(), CompareKM(), PlotRspBar()

Step 2:

Is your biomarker response a dynamic range? Does it have a skewed distribution? Is it correlated with clinical variables?

PlotProperty(), PlotTabForestMulti()

Step 3:

Is your biomarker response associated with a clinical outcome? Is it prognostic or predictive? Is there an optimal biomarker cutoff with a consistent trend?

PlotTabForestBiomarker(), PlotSTEPP()

Step 4:

Estimate the clinical benefit within a biomarker subgroup.

PlotKM(), PlotLong(), PlotRspBar(), CoxTab(), LogRankTab()