TCGAquery_Version

a character string indicating the cancer type for
which to download data. Options include ACC, BLCA, BRCA,
CESC, COAD, DLBC, ESCA, GBM, HNSC, KICH, KIRC, KIRP, LAML,
LGG, LIHC, LUAD, LUSC, OV, PAAD, PRAD, READ, SARC, SKCM, STAD,
THCA, UCEC, UCS. Look at https://tcga-data.nci.nih.gov/tcga/
for Available Cancer Types.

tumor

illuminahiseq_rnaseq, agilentg4502a_07_3,
illuminahiseq_rnaseqv2, humanmethylation27, humanmethylation450,
 illuminaga_mirnaseq, genome_wide_snp_6

platform


As every new version of data has diferent samples and size
the TCGAquery_Version function shows a summary (version, date, number of samples,
size of the data) of all versions of data for a given tumor and platform.


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_Version function

As every new version of data has diferent samples and size
the TCGAquery_Version function shows a summary (version, date, number of samples,
size of the data) of all versions of data for a given tumor and platform.

TCGAquery_Version: Shows a summary (version, date, number of samples, size of the data) of all versions of data for a given tumor and platform.

Description

Usage

Arguments

Value

Examples