## ----include=FALSE------------------------------------------------------------ knitr::opts_chunk$set(eval = FALSE, echo = TRUE) ## ----------------------------------------------------------------------------- # library("sevenbridges") # # create an Auth object # a <- Auth( # url = "https://cgc-datasets-api.sbgenomics.com/", # token = "your_cgc_token" # ) # a$api(path = "datasets") ## ----------------------------------------------------------------------------- # a <- Auth( # url = "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0", # token = "your_cgc_token" # ) # (res <- a$api()) # default method is GET # # list all resources/entities # names(res$"_links") ## ----------------------------------------------------------------------------- # (res <- a$api(path = "files")) ## ----------------------------------------------------------------------------- # a$api(path = "files/schema") ## ----------------------------------------------------------------------------- # (res <- a$api(path = "files")) # # get_id <- function(obj) sapply(obj$"_embedded"$files, function(x) x$id) # ids <- get_id(res) # # # create CGC auth # a_cgc <- Auth(platform = "cgc", token = a$token) # a_cgc$copyFile(id = ids, project = "RFranklin/tcga-demo") ## ----------------------------------------------------------------------------- # body <- list( # entity = "samples", # hasCase = "0004D251-3F70-4395-B175-C94C2F5B1B81" # ) # a$api(path = "query", body = body, method = "POST") ## ----------------------------------------------------------------------------- # a$api(path = "query/total", body = body, method = "POST") ## ----------------------------------------------------------------------------- # httr::content( # api( # token = a$token, # base_url = "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/samples/9259E9EE-7279-4B62-8512-509CB705029C" # ) # ) ## ----------------------------------------------------------------------------- # body <- list( # "entity" = "cases", # "hasAgeAtDiagnosis" = list( # "filter" = list( # "gt" = 10, # "lt" = 50 # ) # ) # ) # a$api(path = "query", body = body, method = "POST") ## ----------------------------------------------------------------------------- # body <- list( # "entity" = "cases", # "hasAgeAtDiagnosis" = list( # "filter" = list( # "gt" = 10, # "lt" = 50 # ) # ), # "hasDiseaseType" = "Kidney Chromophobe" # ) # a$api(path = "query", body = body, method = "POST") ## ----------------------------------------------------------------------------- # body <- list( # "entity" = "cases", # "hasSample" = list( # "hasSampleType" = "Primary Tumor", # "hasPortion" = list( # "hasPortionNumber" = 11 # ) # ), # "hasNewTumorEvent" = list( # "hasNewTumorAnatomicSite" = c("Liver", "Pancreas"), # "hasNewTumorEventType" = list( # "filter" = list( # "contains" = "Recurrence" # ) # ) # ) # ) # a$api(path = "query", body = body, method = "POST") ## ----------------------------------------------------------------------------- # httr::content( # api( # token = a$token, # base_url = "https://cgc-datasets-api.sbgenomics.com/datasets/tcga/v0/cases/0004D251-3F70-4395-B175-C94C2F5B1B81" # ) # ) ## ----------------------------------------------------------------------------- # get_id <- function(obj) sapply(obj$"_embedded"$files, function(x) x$id) # names(res) # # body <- list( # "entity" = "cases", # "hasSample" = list( # "hasSampleType" = "Primary Tumor", # "hasPortion" = list( # "hasPortionNumber" = 11, # "hasID" = "TCGA-DD-AAVP-01A-11" # ) # ), # "hasNewTumorEvent" = list( # "hasNewTumorAnatomicSite" = "Liver", # "hasNewTumorEventType" = "Intrahepatic Recurrence" # ) # ) # # (res <- a$api(path = "files", body = body)) # get_id(res)