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

Description Usage Arguments Value Examples

View source: R/clinical.R

Description

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

Usage

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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

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# 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"))

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