## ---- setup, include=FALSE---------------------------------------------------- knitr::opts_chunk$set(cache = TRUE) ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(cBioPortalData) library(AnVIL) ## ----------------------------------------------------------------------------- cbio <- cBioPortal() studies <- getStudies(cbio, buildReport = TRUE) head(studies) ## ----message=FALSE,warning=FALSE---------------------------------------------- ## Use ask=FALSE for non-interactive use laml <- cBioDataPack("laml_tcga", ask = FALSE) laml ## ----warning=FALSE------------------------------------------------------------ acc <- cBioPortalData(api = cbio, by = "hugoGeneSymbol", studyId = "acc_tcga", genePanelId = "IMPACT341", molecularProfileIds = c("acc_tcga_rppa", "acc_tcga_linear_CNA") ) acc ## ----eval=FALSE--------------------------------------------------------------- # removeCache("laml_tcga") ## ----eval=FALSE--------------------------------------------------------------- # unlink("~/.cache/cBioPortalData/") ## ----message=FALSE,warning=FALSE---------------------------------------------- library(survival) library(survminer) ## ----------------------------------------------------------------------------- table(colData(laml)$OS_STATUS) class(colData(laml)$OS_MONTHS) ## ----------------------------------------------------------------------------- collaml <- colData(laml) collaml[collaml$OS_MONTHS == "[Not Available]", "OS_MONTHS"] <- NA collaml$OS_MONTHS <- as.numeric(collaml$OS_MONTHS) colData(laml) <- collaml ## ----------------------------------------------------------------------------- fit <- survfit( Surv(OS_MONTHS, as.numeric(substr(OS_STATUS, 1, 1))) ~ SEX, data = colData(laml) ) ggsurvplot(fit, data = colData(laml), risk.table = TRUE) ## ----------------------------------------------------------------------------- sessionInfo()