curatedPCaDatasets_igc: International Genomics Consortium (IGC) MAE-object

In Syksy/curatedPCaData: Curated Prostate Cancer Data

International Genomics Consortium (IGC) MAE-object

Description

MultiAssayExperiment object containing gene expression (gex) and immune cell estimates from IGC's Expression Project for Oncology (expO) with a subset for prostate cancer

Format

An MAE object spanning 83 men with prostate cancer

gex.rma

matrix with 12798 rows and 83 columns, of gene expression data

cibersort

matrix with 22 rows and 83 columns, of cibersort based deconvolution data

xcell

matrix with 39 rows and 83 columns, of xcell based deconvolution data

epic

matrix with 8 rows and 83 columns, of epic based deconvolution data

quantiseq

matrix with 11 rows and 83 columns, of quantiseq based deconvolution data

estimate

data.frame with 4 rows and 83 columns, of cell types based on ESTIMATE method

scores

matrix with 4 rows and 83 columns, of risk scores and AR scores

mcp

matrix with 11 rows and 83 columns, of mcp-counter based deconvolution data

Value

A MultiAssayExperiment corresponding to the study and its available omics.

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2109

Examples

mae_igc <- getPCa('igc')

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