showCancerStudy: List of cancer studies included in the cBioportal

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

Description

Show all the possible cancer studies accepted by PrecisionTrialDrawer

Usage

showCancerStudy(tumor_type=NULL)

Arguments

tumor_type

a valid tumor type barcode in TCGA standard coding

Details

This method is a wrapper around cgdsr-getCancerStudies and show all the cancer studies included in the cBioPortal. If you specify the tumor_type, follow the list of showTumorType. Even though the cancer studies are present, it doesn't mean that there are data for every alteration. A tumor type could have mutation data but not copynumber or viceversa. Furthermore, fusion data have a different source and could not be included in the list.

Value

A named vector of all the cancer studies available in cgdsr package that can be passed to the method getAlterations.

Author(s)

Giorgio Melloni, Alessandro Guida

See Also

getAlterations showTumorType cgdsr-getCancerStudies

Examples

myCanStudies <- showCancerStudy()
head(myCanStudies)

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