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Firstly, assume you have already installed UCSCXenaShiny package.

library(UCSCXenaShiny)
#> =========================================================================================
#> UCSCXenaShiny version 2.1.0
#> 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--

Tutorial Book

From UCSCXenaShiny v2, we provide a comprehensive tutorial book for introducing how to use the datasets, functions, and the Shiny application.

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", "methylation", "miRNA", "fusion", "promoter", 
#>     "APOBEC"), database = c("toil", "ccle", "pcawg"), reset_id = NULL, 
#>     opt_pancan = .opt_pancan) 
#> 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 1.4.8
#> 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 cite:
#> Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
#>   from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
#>   Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
#> =========================================================================================
#>                               --Enjoy it--
#> Try querying data #1
#> -> Checking if the dataset has probeMap...
#> -> Done. ProbeMap is found.
#> Saving data to file /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh80000gn/T//RtmptASQAZ/UCSCXenaShiny/4822f991b17cbdab3831c455be7620b2.rds
#> More info about dataset please run following commands:
#>   library(UCSCXenaTools)
#>   XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_rsem_gene_tpm") %>% XenaBrowse()
str(gene_expr)
#> List of 2
#>  $ expression: Named num [1:19131] 4.79 5.89 5.52 4.43 2.38 ...
#>   ..- attr(*, "names")= chr [1:19131] "GTEX-S4Q7-0003-SM-3NM8M" "TCGA-19-1787-01" "TCGA-S9-A7J2-01" "GTEX-QV31-1626-SM-2S1QC" ...
#>   ..- attr(*, "label")= chr "gene expression RNAseq"
#>  $ unit      : chr "log2(tpm+0.001)"

Fetch Transcript Expression

transcript_expr <- query_pancan_value("ENST00000000233", data_type = "transcript")

Fetch Gene CNV

gene_cnv <- query_pancan_value("TP53", data_type = "cnv")

Fetch Gene Mutation

gene_mut <- query_pancan_value("TP53", data_type = "mutation")

Fetch miRNA mature strand expression

miRNA_expr <- query_pancan_value("hsa-let-7a-2-3p", data_type = "miRNA")

Data Visualization

Visualize Single Gene Expression in PANCAN Dataset

vis_toil_TvsN(Gene = "TP53", Mode = "Violinplot", Show.P.value = FALSE, Show.P.label = FALSE)
#> Reading cache data /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh80000gn/T//RtmptASQAZ/UCSCXenaShiny/4822f991b17cbdab3831c455be7620b2.rds
#> More info about dataset please run following commands:
#>   library(UCSCXenaTools)
#>   XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_rsem_gene_tpm") %>% XenaBrowse()

Compare Gene Expression Level in Single Cancer Type

vis_toil_TvsN_cancer(
  Gene = "TP53",
  Mode = "Violinplot",
  Show.P.value = TRUE,
  Show.P.label = TRUE,
  Method = "wilcox.test",
  values = c("#DF2020", "#DDDF21"),
  TCGA.only = FALSE,
  Cancer = "ACC"
)
#> Reading cache data /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh80000gn/T//RtmptASQAZ/UCSCXenaShiny/4822f991b17cbdab3831c455be7620b2.rds
#> More info about dataset please run following commands:
#>   library(UCSCXenaTools)
#>   XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_rsem_gene_tpm") %>% XenaBrowse()
#> Counting P value
#> Counting P value finished

Compare Gene Expression Level in Different Anatomic Regions

This function needs gganatogram package, which is not on CRAN. Please install it before using this function.

if (require("gganatogram")) {
  vis_pancan_anatomy(Gene = "TP53", Gender = c("Female", "Male"), option = "D")
}

Click to see the output

Visualize Relationship between Gene Expression and Prognosis in the PANCAN Dataset

vis_unicox_tree(
  Gene = "TP53",
  measure = "OS",
  threshold = 0.5,
  values = c("grey", "#E31A1C", "#377DB8")
)
#> Reading cache data /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh80000gn/T//RtmptASQAZ/UCSCXenaShiny/4822f991b17cbdab3831c455be7620b2.rds
#> More info about dataset please run following commands:
#>   library(UCSCXenaTools)
#>   XenaGenerate(subset = XenaDatasets == "TcgaTargetGtex_rsem_gene_tpm") %>% XenaBrowse()
#> Get data value for TP53

Other Functions and Data

All exported data and functions are organized at here.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.