GDCquery_clinic: Get GDC clinical data

Description Usage Arguments Value Examples

View source: R/clinical.R

Description

GDCquery_clinic will download all clinical information from the API as the one with using the button from each project

Usage

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GDCquery_clinic(project, type = "clinical", save.csv = FALSE)

Arguments

project

A valid project (see list with getGDCprojects()$project_id)]

  • BEATAML1.0-COHORT

  • BEATAML1.0-CRENOLANIB

  • CGCI-BLGSP

  • CPTAC-2

  • CPTAC-3

  • CTSP-DLBCL1

  • FM-AD

  • HCMI-CMDC

  • MMRF-COMMPASS

  • NCICCR-DLBCL

  • OHSU-CNL

  • ORGANOID-PANCREATIC

  • TARGET-ALL-P1

  • TARGET-ALL-P2

  • TARGET-ALL-P3

  • TARGET-AML

  • TARGET-CCSK

  • TARGET-NBL

  • TARGET-OS

  • TARGET-RT

  • TARGET-WT

  • TCGA-ACC

  • TCGA-BLCA

  • TCGA-BRCA

  • TCGA-CESC

  • TCGA-CHOL

  • TCGA-COAD

  • TCGA-DLBC

  • TCGA-ESCA

  • TCGA-GBM

  • TCGA-HNSC

  • TCGA-KICH

  • TCGA-KIRC

  • TCGA-KIRP

  • TCGA-LAML

  • TCGA-LGG

  • TCGA-LIHC

  • TCGA-LUAD

  • TCGA-LUSC

  • TCGA-MESO

  • TCGA-OV

  • TCGA-PAAD

  • TCGA-PCPG

  • TCGA-PRAD

  • TCGA-READ

  • TCGA-SARC

  • TCGA-SKCM

  • TCGA-STAD

  • TCGA-TGCT

  • TCGA-THCA

  • TCGA-THYM

  • TCGA-UCEC

  • TCGA-UCS

  • TCGA-UVM

  • VAREPOP-APOLLO

type

A valid type. Options "clinical", "Biospecimen" (see list with getGDCprojects()$project_id)]

save.csv

Write clinical information into a csv document

Value

A data frame with the clinical information

Examples

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clin <- GDCquery_clinic("TCGA-ACC", type = "clinical", save.csv = TRUE)
clin <- GDCquery_clinic("TCGA-ACC", type = "biospecimen", save.csv = TRUE)
clin.cptac2 <- GDCquery_clinic("CPTAC-2", type = "clinical")
clin.TARGET_ALL_P1 <- GDCquery_clinic("TARGET-ALL-P1", type = "clinical")
clin.fm_ad <- GDCquery_clinic("FM-AD", type = "clinical")
## Not run: 
clin <- GDCquery_clinic(project = "CPTAC-3", type = "clinical")
clin <- GDCquery_clinic(project = "CPTAC-2", type = "clinical")
clin <- GDCquery_clinic(project = "HCMI-CMDC", type = "clinical")
clin <- GDCquery_clinic(project = "NCICCR-DLBCL", type = "clinical")
clin <- GDCquery_clinic(project = "ORGANOID-PANCREATIC", type = "clinical")

## End(Not run)

daniel615212950/TCGAbiolinks documentation built on Dec. 19, 2021, 8:06 p.m.