Firstly, assume you have already installed UCSCXenaShiny package.

library(UCSCXenaShiny)
#> =========================================================================================
#> UCSCXenaShiny version 1.1.3
#> Project URL: https://github.com/openbiox/UCSCXenaShiny
#> Usages: https://openbiox.github.io/UCSCXenaShiny/
#> 
#> If you use it in published research, please cite:
#>   Shixiang Wang, Yi Xiong, Longfei Zhao, Kai Gu, Yin Li, Fei Zhao, Jianfeng Li,
#>   Mingjie Wang, Haitao Wang, Ziyu Tao, Tao Wu, Yichao Zheng, Xuejun Li, Xue-Song Liu,
#>   UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data, 
#>   Bioinformatics, 2021;, btab561, https://doi.org/10.1093/bioinformatics/btab561.
#> =========================================================================================
#>                               --Enjoy it--

Fetch Data

We provide function to retrieve multi-dimensional data including genomic, epigenomic, transcriptomic, and proteomic data from TCGA (note, this actually contains data from TCGA/TARGET/GTEx databases) and CCLE Pan-Cancer dataset for single identifier (e.g., gene, protein).

Check parameters:

args(query_pancan_value)
#> function (molecule, data_type = c("mRNA", "transcript", "protein", 
#>     "mutation", "cnv", "cnv_gistic2", "methylation", "miRNA", 
#>     "fusion", "promoter", "APOBEC"), database = c("toil", "ccle", 
#>     "pcawg"), reset_id = NULL, ...) 
#> NULL

For TCGA gene expression data, we use Xena dataset with ID TcgaTargetGtex_rsem_gene_tpm which includes 19131 samples with tumor tissue samples and normal tissue samples. The expression value unit is log2(tpm+0.001).

Let’s check several examples.

Fetch Gene Expression

gene_expr <- query_pancan_value("TP53")
#> =========================================================================================
#> UCSCXenaTools version 1.4.7
#> Project URL: https://github.com/ropensci/UCSCXenaTools
#> Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
#> 
#> If you use it in published research, please cit