| Title: | Processed Harmonized TCGA Data of Five Selected Cancer Types |
|---|---|
| Description: | This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering". |
| Authors: | Tianle Ma |
| Maintainer: | Tianle Ma <[email protected]> |
| License: | GPL-3 |
| Version: | 1.34.0 |
| Built: | 2026-10-10 11:10:47 UTC |
| Source: | https://github.com/bioc/HarmonizedTCGAData |
A named character vector: mapping case_id (i.e., patient ID) to the TCGA project ID they belong to
project_idsproject_ids
An object of class character of length 14551.
library(ExperimentHub) eh <- ExperimentHub() myfiles <- query(eh, "HarmonizedTCGAData") project_ids <- myfiles[[2]] # project_ids <- myfiles[['EH1015']] head(project_ids)library(ExperimentHub) eh <- ExperimentHub() myfiles <- query(eh, "HarmonizedTCGAData") project_ids <- myfiles[[2]] # project_ids <- myfiles[['EH1015']] head(project_ids)
Patient survival information (overall survival plot data) were downloaded from https://portal.gdc.cancer.gov/exploration?searchTableTab=genes For detailed information: see section "Survival analysis" in https://docs.gdc.cancer.gov/Data_Portal/PDF/Data_Portal_UG.pdf
surv.plotsurv.plot
A data frame with four variables: survivalEstimate, id,
censored, and time
library(ExperimentHub) eh <- ExperimentHub() myfiles <- query(eh, "HarmonizedTCGAData") surv.plot <- myfiles[[3]] # surv.plot <- myfiles[['EH1016']] head(surv.plot)library(ExperimentHub) eh <- ExperimentHub() myfiles <- query(eh, "HarmonizedTCGAData") surv.plot <- myfiles[[3]] # surv.plot <- myfiles[['EH1016']] head(surv.plot)
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).
WallWall
An object of class list of length 5.
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]])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]])