TCGAquery_SampleTypes

barcode

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

typesample


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


The aim of TCGAbiolinks is : i) facilitate the TCGA open-access
data retrieval, ii) prepare the data using the appropriate pre-processing
strategies, iii) provide the means to carry out different standard analyses
and iv) allow the user to download a specific version of the data and thus
to easily reproduce earlier research results. In more detail, the package
provides multiple methods for analysis (e.g., differential expression analysis,
identifying differentially methylated regions) and methods for visualization
(e.g., survival plots, volcano plots, starburst plots) in order to easily
develop complete analysis pipelines.

Antonio Colaprico

TCGAbiolinks

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

TCGAquery_SampleTypes function

a character vector indicating tissue type to query.
Example:
<tabular>ll</tabular>{
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 }

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

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

Description

Usage

Arguments

Value

Examples