Examples of Accessible Functions

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center"
)

Firstly, assume you have already installed UCSCXenaShiny package.

library(UCSCXenaShiny)

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)

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")
str(gene_expr)

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

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"
)

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")
)

Other Functions and Data

All exported data and functions are organized at here.



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