## ----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()