inst/doc/CVE_tutorial.R

In CVE: Cancer Variant Explorer

## ----eval=FALSE------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install('CVE')

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

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

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

## --------------------------------------------------------------------------
#pick a single patient for case study
mutData <- selectType(crcData, "Mutation")
crcCase_Firehouse <- mutData[mutData[["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[1:100,])

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

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

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