GDCquery_clinic: Get GDC clinical data

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Description

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

Usage

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

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)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.