load_data {UCSCXenaShiny}R Documentation

Load Dataset Provided by This Package

Description

Load data from builtin or Zenodo. Option xena.zenodoDir can be used to set default path for storing extra data from Zenodo, e.g., options(xena.zenodoDir = "/home/xxx/dataset").

Usage

load_data(name)

Arguments

name

a dataset name. Could be one of

Builtin datasets:

  • ccle_absolute: CCLE ABSOLUTE result.

  • ccle_info: CCLE information.

  • ccle_info_fine: cleaned CCLE information for TPC analysis.

  • pcawg_info: PCAWG information.

  • pcawg_info_fine: cleaned PCAWG information for TPC analysis.

  • pcawg_purity: PCAWG tumor purity, ploidy and WGD data.

  • tcga_clinical: TCGA clinical data.

  • tcga_clinical_fine: cleaned TCGA information for TPC analysis.

  • tcga_genome_instability: TCGA genome instability data.

  • tcga_gtex: TCGA and GTEX sample info.

  • tcga_purity: TCGA tumor purity data.

  • tcga_subtypes: TCGA subtypes data.

  • tcga_surv: TCGA survival data.

  • TCGA.organ: TCGA organ data.

  • toil_info: Toil hub information.

Remote datasets stored in Zenodo:

  • pcawg_promoter_id: PCAWG promoter identifiers.

  • transcript_identifier: Common transcript identifiers.

  • ccle_expr_and_drug_response: CCLE expression and drug response data.

  • ccle_drug_response_extend: CCLE drug response extended data.

  • pancan_MSI: Pan-cancer MSI data.

  • tcga_chr_alteration: TCGA chromosome alteration data.

  • tcga_MSI: TCGA MSI data.

  • tcga_pan_immune_signature: TCGA pan-cancer immune signature.

  • tcga_stemness: TCGA tumor stemness data.

  • tcga_TIL: TCGA TIL data.

  • tcga_PW: ssGSEA scores of HALLMARK, KEGG, IOBR terms for TCGA samples.

  • tcga_PW_meta: metadata annotation for HALLMARK, KEGG, IOBR terms.

  • tcga_tmb: TCGA TMB data.

  • tcga_armcalls: TCGA arm alteration calls and Aneuploidy data.

  • tcga_dna_repair: TCGA DNA repair data.

  • pancancer_conserved_immune_subtype: Pan-cancer conserved immune subtypes.

  • pcawg_TIL: PCAWG TIL data.

  • pcawg_PW: ssGSEA scores of HALLMARK, KEGG, IOBR terms for PCAWG samples.

  • ...

Value

a dataset, typically a data.frame.

Examples

data1 <- load_data("tcga_surv")
data1

data2 <- load_data("tcga_armcalls")
data2
[Package UCSCXenaShiny version 2.1.0 Index]