PrecisionTrialDrawer-package: PrecisionTrialDrawer: a package to analyze and design custom...

In PrecisionTrialDrawer: A Tool to Analyze and Design NGS Based Custom Gene Panels

Description

PrecisionTrialDrawer is a package that a allows the design and study of a cancer panel to create pilot sets for a clinical trial.

Details

It allows simulations on real TCGA data to design a possible clinical trial, both as basket or umbrella design.

Furthermore, it can provide an easy function to calculate genomic space occupied by the cancer panel in a commonly used bed format ready to be submitted to a NGS company.

Author(s)

Giorgio Melloni, Alessandro Guida

References

Cbioportal web site MD Anderson TCGA Fusion Portal

Examples

# Retrieve a Cancer Panel 
data(cpObj)
# Show the number of covered samples
coveragePlot(cpObj 
            , alterationType=c("mutations" , "copynumber") 
            , grouping=c("group" , "tumor_type"))

PrecisionTrialDrawer documentation built on Nov. 8, 2020, 8:17 p.m.