load_data: Load Dataset Provided by This Package

Description Usage Arguments Value Examples

View source: R/load_data.R

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

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Arguments

name

a dataset name. Could be one of

Builtin datasets:

  • ccle_absolute: CCLE ABSOLUTE result.

  • ccle_info: CCLE information.

  • pcawg_info: PCAWG information.

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

  • tcga_clinical: TCGA clinical data.

  • 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_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.

Value

a dataset, typically a data.frame.

Examples

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data1 <- load_data("tcga_surv")
data1

data2 <- load_data("tcga_armcalls")
data2

UCSCXenaShiny documentation built on Nov. 29, 2021, 9:06 a.m.