## ----eval=FALSE----------------------------------------------------------
#  source('http://www.bioconductor.org/biocLite.R')
#  biocLite('CVE')

## ----eval=FALSE----------------------------------------------------------
#  library(CVE)

## ----message=FALSE-------------------------------------------------------
#load package
library(RTCGAToolbox)

#load all colorectal cancer data 
crcData = getFirehoseData(dataset="COAD",
                          Clinic=TRUE,
                          Mutation=TRUE,
                          runDate="20160128")

## ------------------------------------------------------------------------
#pick a single patient for case study
crcCase_Firehouse = crcData@Mutations[crcData@Mutations$Tumor_Sample_Barcode=="TCGA-AA-A00N-01A-02W-A00E-09",]

## ------------------------------------------------------------------------
crcCase_input = data.frame(chr=crcCase_Firehouse$Chromosome,
                      start=crcCase_Firehouse$Start_position,
                      end=crcCase_Firehouse$End_position,
                      reference_allele=crcCase_Firehouse$Reference_Allele,
                      observed_allele=crcCase_Firehouse$Tumor_Seq_Allele2)
head(crcCase_input)

## ----eval=FALSE----------------------------------------------------------
#  library(jsonlite)
#  crcCase = get.oncotator.anno(crcCase_input)

## ---- eval=FALSE---------------------------------------------------------
#  openCVE(crcCase)

## ---- eval=FALSE---------------------------------------------------------
#  openCVE(melanomaCase, extension="WGCNAmelanoma")

## ------------------------------------------------------------------------
sessionInfo()