TCGAbiolinks (version 1.2.5)

TCGAquery_clinic: Get the clinical information

Description

Get the clinical information

Usage

TCGAquery_clinic(tumor, clinical_data_type, samples, path = getwd())

Arguments

tumor

a character vector indicating cancer type Examples:

OV	BRCA	CESC	ESCA
PCPG	LUSC	LGG	SKCM
KICH	CHOL	GBM	UCEC
PRAD	PAAD	THYM	KIRC
THCA	SARC	LAML	TGCT
COAD	KIRP	HNSC	ACC
UVM	READ	BLCA	DLBC
UCS	FPPP	OV	BRCA

For information about cancer types: https://tcga-data.nci.nih.gov/tcga/

clinical_data_type

a character vector indicating the types of clinical data Example:

biospecimen_aliquot

biospecimen_analyte

biospecimen_cqcf

biospecimen_diagnostic_slides

biospecimen_normal_control

biospecimen_portion

biospecimen_protocol

biospecimen_sample

biospecimen_shipment_portion

biospecimen_slide

biospecimen_tumor_sample

clinical_cqcf

clinical_follow_up_v1.0

clinical_follow_up_v1.5

clinical_follow_up_v2.0

clinical_follow_up_v2.1

clinical_follow_up_v4.0

clinical_follow_up_v4.0_nte

clinical_nte

clinical_omf_v4.0

clinical_patient

clinical_radiation

ssf_normal_controls

ssf_tumor_samples

clinical_follow_up_v1.0_nte

samples

List of barcodes to get the clinical data

path

Directory to save the downloaded data default getwd()

Value

clinic data

Examples

data <- TCGAquery_clinic("LGG","clinical_drug")
data <- TCGAquery_clinic(clinical_data_type = "clinical_patient",
samples = c("TCGA-06-5416-01A-01D-1481-05",
            "TCGA-2G-AAEW-01A-11D-A42Z-05",
            "TCGA-2G-AAEX-01A-11D-A42Z-05"))