UCSCXenaShiny (version 2.1.0)

load_data: 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)

Value

a dataset, typically a data.frame.

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.

• ...

Examples

data1 <- load_data("tcga_surv")
data1
# \donttest{
data2 <- load_data("tcga_armcalls")
data2
# }