TCGAquery_SampleTypes: Retrieve multiple tissue types not from the same patients.

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

Retrieve multiple tissue types not from the same patients.

Description

TCGAquery_SampleTypes for a given list of samples and types, return the union of samples that are from theses type.

Usage

TCGAquery_SampleTypes(barcode, typesample)

Arguments

barcode

is a list of samples as TCGA barcodes

typesample

a character vector indicating tissue type to query. Example: TP PRIMARY SOLID TUMOR TR RECURRENT SOLID TUMOR TB Primary Blood Derived Cancer-Peripheral Blood TRBM Recurrent Blood Derived Cancer-Bone Marrow TAP Additional-New Primary TM Metastatic TAM Additional Metastatic THOC Human Tumor Original Cells TBM Primary Blood Derived Cancer-Bone Marrow NB Blood Derived Normal NT Solid Tissue Normal NBC Buccal Cell Normal NEBV EBV Immortalized Normal NBM Bone Marrow Normal

Value

a list of samples / barcode filtered by type sample selected

Examples

# selection of normal samples "NT"
barcode <- c("TCGA-B0-4698-01Z-00-DX1","TCGA-CZ-4863-02Z-00-DX1")
# Returns the second barcode
 TCGAquery_SampleTypes(barcode,"TR")
 # Returns both barcode
 TCGAquery_SampleTypes(barcode,c("TR","TP"))
 barcode <- c("TARGET-20-PANSBH-14A-02D","TARGET-20-PANSBH-01A-02D",
              "TCGA-B0-4698-01Z-00-DX1","TCGA-CZ-4863-02Z-00-DX1")
  TCGAquery_SampleTypes(barcode,c("TR","TP"))

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.