Wall: Wall

In BeautyOfWeb/HarmonizedTCGAData: Processed Harmonized TCGA Data of Five Selected Cancer Types

Description

Wall contains a list of precomputed affinity (similarity) matrices of 2582 patients. These matrices were derived from 10382 gene expression, miRNA expression and DNA methylation data files downloaded from GDC data portal The file UUIDs can be found in inst/extdata/fileUUIDs.csv Using these file UUIDs, users can download the original data from https://portal.gdc.cancer.gov/repository 'Wall' is a complex list and contains lists inside list. Precisely, Wall is a list (five cancer types) of list (six feature normalization types: raw.all, raw.sel, log.all, log.sel, vst.sel, normalized) of list (three feature spaces or views: fpkm, mirna, and methy450) of matrices. (So Wall contains 90 matrices in total) The rownames of each matrix is the case_id (i.e., patient id), and the column names of each matrix is the aliquot IDs (i.e., TCGA barcode, which contains the case_id as prefix).

Usage

Wall

Format

An object of class list of length 5.

Examples

library(ExperimentHub)
eh <- ExperimentHub()
myfiles <- query(eh, "HarmonizedTCGAData")
Wall <- myfiles[[1]]
# Wall <- myfiles[['EH1014']]
names(Wall)
names(Wall[[1]])
names(Wall[[1]][[1]])
dim(Wall[[1]][[1]][[1]])

BeautyOfWeb/HarmonizedTCGAData documentation built on May 28, 2019, 11:57 a.m.