getPCaSummaryTable: Create summary tables for colData metadata in curatedPCaData

In Syksy/curatedPCaData: Curated Prostate Cancer Data

Create summary tables for colData metadata in curatedPCaData

Description

Create a variable value availability tables; NA-value in addition to provided 'vals' and Other-values for debugging or anomalies

Usage

getPCaSummaryTable(maes, var.name, vals, nas = TRUE)

Arguments

maes	List of MultiAssayExperiment objects to summarize
var.name	Name of the metadata variable to look for in colData
vals	Possible values for the metadata variable to tabulate
nas	Whether NA or values other than those contained in 'vals' should be appended as extra columns

Value

A matrix describing the tabulates 'vals' and their proportions along with missingness

Examples

mae_taylor <- getPCa('taylor')
mae_tcga <- getPCa('tcga')
getPCaSummaryTable(maes = list(Taylor = mae_taylor, TCGA = mae_tcga), 
    var.name = 'gleason_grade', vals = 5:10)

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