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

Run this code
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"))

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