inst/doc/cgc-datasets.R

In sevenbridges: Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

## ----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)