curatedPCaDatasets_tcga: TCGA MAE-object

In Syksy/curatedPCaData: Curated Prostate Cancer Data

TCGA MAE-object

Description

MultiAssayExperiment object containing gene expression (gex), copy number alteration (cna), mutations and immune cell estimates from GDC TCGA.

Format

An MAE object spanning 369 men with prostate cancer

cna.gistic

matrix with 23151 rows and 492 columns, from GISTIC discretized copy number alteration calls

gex.rsem.log

matrix with 19658 rows and 461 columns, of gene expression data

mut

RaggedExperiment with 30897 rows and 495 columns, of mutation data

cibersort

matrix with 22 rows and 550 columns, of cibersort based deconvolution data

xcell

matrix with 39 rows and 461 columns, of xcell based deconvolution data

epic

matrix with 8 rows and 461 columns, of epic based deconvolution data

quantiseq

matrix with 11 rows and 461 columns, of quantiseq based deconvolution data

mcp

matrix with 11 rows and 461 columns, of mcp-counter based deconvolution data

estimate

data.frame with 4 rows and 461 columns, of cell types based on ESTIMATE method

scores

matrix with 4 rows and 416 columns, of risk scores and AR scores

Details

TCGA data was obtained from the latest GDC's XenaBrowser release.

Value

A MultiAssayExperiment corresponding to the study and its available omics.

Source

https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Prostate%20Cancer%20(PRAD)

References

(PubMed)

Examples

mae_tcga <- getPCa('tcga')

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