curatedPCaDatasets_barbieri: Barbieri et al. MAE-object
In Syksy/curatedPCaData: Curated Prostate Cancer Data

curatedPCaDatasets_barbieri

R Documentation

Barbieri et al. MAE-object

Description

MultiAssayExperiment object containing gene expression (gex), copy number alteration (cna), mutations (mut) and immune cell estimates for Barbieri et al.

Format

A MAE object spanning prostate adenocarcinomas from Barbieri et. al

cna.gistic: matrix with 20844 rows and 109 columns, from GISTIC discretized copy number alteration calls
gex.relz: matrix with 17917 rows and 31 columns, from z-score normalized expression in relative to paired normals.
mut: RaggedExperiment with 5737 rows and 112 columns, mutation data from cbioportal
cibersort: matrix with 22 rows and 31 columns, of cibersort based deconvolution data
xcell: matrix with 39 rows and 31 columns, of xcell based deconvolution data
epic: matrix with 8 rows and 31 columns, of epic based deconvolution data
quantiseq: matrix with 11 rows and 31 columns, of quantiseq based deconvolution data
estimate: data.frame with 4 rows and 31 columns, of cell types based on ESTIMATE method
scores: matrix with 4 rows and 31 columns, of risk scores and AR scores
mcp: matrix with 11 rows and 31 columns, of mcp-counter based deconvolution data

Details

The data comprises of primary localised prostate tumors from two cohorts, the Weill Cornell Medical College (WCMC; New York, NY), and the Uropath (Perth, Australia), which commercially provides banked urological tissues. None of the samples comes from patients who had received prior treatment for prostate cancer.