curatedPCaDatasets_ren: Ren et al. MAE-object

In Syksy/curatedPCaData: Curated Prostate Cancer Data

Ren et al. MAE-object

Description

MultiAssayExperiment object containing gene expression (gex), mutations and immune cell estimates from Ren et al.

Format

An MAE object spanning 65 men with prostate cancer

gex.relz

matrix with 21046 rows and 65 columns, of gene expression data

mut

RaggedExperiment with 50625 rows and 65 columns, of mutation data from cbioportal

cibersort

matrix with 22 rows and 65 columns, of cibersort based deconvolution data

xcell

matrix with 39 rows and 65 columns, of xcell based deconvolution data

epic

matrix with 8 rows and 65 columns, of epic based deconvolution data

quantiseq

matrix with 11 rows and 65 columns, of quantiseq based deconvolution data

estimate

data.frame with 4 rows and 65 columns, of cell types based on ESTIMATE method

scores

matrix with 4 rows and 65 columns, of risk scores and AR scores

mcp

matrix with 11 rows and 65 columns, of mcp-counter based deconvolution data

Details

The data contains 14 disease free benign prostate hyperplasia samples and 53 prostate cancer samples.

Value

A MultiAssayExperiment corresponding to the study and its available omics.

Source

https://www.cbioportal.org/study/summary?id=prad_eururol_2017

References

(PubMed)

Examples

mae_ren <- getPCa('ren')

Syksy/curatedPCaData documentation built on Nov. 4, 2023, 9:46 a.m.