Examples of Accessible Functions

  collapse = TRUE,
  comment = "#>",
  fig.align = "center"

Firstly, assume you have already installed UCSCXenaShiny package.


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:


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")

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)

Compare Gene Expression Level in Single Cancer Type

  Gene = "TP53",
  Mode = "Violinplot",
  Show.P.value = TRUE,
  Show.P.label = TRUE,
  Method = "wilcox.test",
  values = c("#DF2020", "#DDDF21"),
  TCGA.only = FALSE,
  Cancer = "ACC"

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

  Gene = "TP53",
  measure = "OS",
  threshold = 0.5,
  values = c("grey", "#E31A1C", "#377DB8")

Other Functions and Data

All exported data and functions are organized at here.

Try the UCSCXenaShiny package in your browser

Any scripts or data that you put into this service are public.

UCSCXenaShiny documentation built on July 30, 2021, 9:10 a.m.