showTumorType: List of tumor type barcode

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

Description

Show all the possible tumor types accepted by PrecisionTrialDrawer

Usage

showTumorType()

Details

This method is a wrapper around cgdsr-getCancerStudies and show all the barcodes for the tumor types included in the cBioPortal. Even though the tumor types 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 data.frame of all the tumor types available in cgdsr package that can be passed to the method getAlterations. Every element is the aggregation of all the available sequenced data from all the studies involved in a particular tumor type.

Author(s)

Giorgio Melloni, Alessandro Guida

See Also

getAlterations showCancerStudy cgdsr-getCancerStudies

Examples

myTumTypes <- showTumorType()
head(myTumTypes)

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