vis_gene_cross_omics: Visualize cross-omics of one gene among pan-cancers
In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

vis_gene_cross_omics

R Documentation

Visualize cross-omics of one gene among pan-cancers

Description

Visualize cross-omics of one gene among pan-cancers

Usage

vis_gene_cross_omics(
  gene = "TP53",
  tumor_projects = NULL,
  tumor_samples = NULL,
  n_trans = 5,
  n_methy = 5,
  seed = 42,
  add_mean_trans = TRUE,
  add_mean_methy = TRUE,
  pval_mrna = c(0.05, 0.01, 0.001),
  return_list = FALSE
)

Arguments

`gene`	a gene symbol identifier (e.g., "TP53")
`tumor_projects`	Select specific TCGA projects. Default NULL, indicating all TCGA projects.
`tumor_samples`	Select specific tumor samples. Default NULL, indicating all tumor samples.
`n_trans`	The number of sampling transcripts or specific transcript identifiers.
`n_methy`	The number of sampling CpG sites or specific CpG identifiers.
`seed`	The seed of sampling.
`add_mean_trans`	Add overall column to display the mean values of all gene's transcripts.
`add_mean_methy`	Add overall column to display the mean values of all gene's cpg sites.
`pval_mrna`	The P value thresholds
`return_list`	TRUE returns a list including plot object and data. FALSE just returns plot.