getPCaSummarySamples: Create a summary table for sample counts for different omics...

In Syksy/curatedPCaData: Curated Prostate Cancer Data

Create a summary table for sample counts for different omics across the datasets in curatedPCaData

Description

Create two types of summary matrices; first one takes all unique assay names, and summarizes sample counts available for all provided studies. The second matrix takes gene expression, copy number alteration, and somatic mutation data, and displays sample counts for each omic individually, as well as all combinations of intersections for samples available for multi-omics.

Usage

getPCaSummarySamples(maes)

Arguments

maes	List of MultiAssayExperiment objects to summarize

Value

A list with two elements: first is a matrix depicting sample counts in each unique assay name for the studies; second one is a matrix with sample count overlap between the three main omics (GEX = gene expression; CNA = copy number alteration; MUT = somatic mutations).

Examples

mae_taylor <- getPCa('taylor')
mae_tcga <- getPCa('tcga')
getPCaSummarySamples(maes = list(Taylor = mae_taylor, TCGA = mae_tcga))

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