curatedPCaDatasets_abida: Abida et al. MAE-object

In Syksy/curatedPCaData: Curated Prostate Cancer Data

Abida et al. MAE-object

Description

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

Format

A MAE object spanning 444 castrate resistant prostate cancer samples.

cna.gistic

matrix with 20291 rows and 444 columns, from GISTIC discretized copy number alteration calls.

gex.relz

matrix with 18971 rows and 266 columns, from z-score normalized expression in relative to paired normals.

mut

RaggedExperiment with 63184 rows and 444 columns, mutation data from cbioportal

cibersort

matrix with 22 rows and 261 columns, of cibersort based deconvolution data

xcell

matrix with 39 rows and 261 columns, of xcell based deconvolution data

epic

matrix with 8 rows and 261 columns, of epic based deconvolution data

quantiseq

matrix with 11 rows and 261 columns, of quantiseq based deconvolution data

estimate

data.frame with 4 rows and 261 columns, of cell types based on ESTIMATE method

scores

matrix with 4 rows and 261 columns, of risk scores and AR scores

mcp

mmatrix with 11 rows and 261 columns, of mcp-counter based deconvolution data

Details

the clinical data refers to a sample of 444 tumors collected in 429 patients. The tissue was collected primarily at metastatic sites rather than from the prostate.

Value

A MultiAssayExperiment corresponding to the study and its available omics.

Source

https://www.cbioportal.org/study/summary?id=prad_su2c_2019

References

(PubMed)

Examples

mae_abida <- getPCa('abida')

Syksy/curatedPCaData documentation built on Oct. 11, 2024, 7:05 a.m.