showTumorType: List of tumor types

In gmelloni/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Description

Show all the possible tumor types accepted by LowMACA

Usage

showTumorType()

Details

This method is a wrapper around cgdsr-getCancerStudies and show all the barcodes for the tumor types as used by cBioPortal.

Value

A named vector of all the tumor types available in cgdsr package that can be passed to the method lmParams. Every element is the aggregation of all the available sequenced data from all the studies involved in a particular tumor type.

Author(s)

Stefano de Pretis , Giorgio Melloni

See Also

lmParams cgdsr-getCancerStudies

Examples

data('lmObj')
out <- showTumorType()
chosenTumors <- out[1:3]
lmParams(lmObj)$tumor_type <- chosenTumors

gmelloni/LowMACA documentation built on May 24, 2019, 5:03 a.m.