curatedTCGAData-helpers {TCGAutils}R Documentation

Helper functions for managing MultiAssayExperiment from curatedTCGAData

Description

Additional helper functions for cleaning and uncovering metadata within a downloaded MultiAssayExperiment from curatedTCGAData. The getSubtypeMap function provides a 2 column data.frame with in-data variable names and an interpreted names. The getClinicalNames function provides a vector of variable names that exist in the colData slot of a downloaded MultiAssayExperiment object. These variables are obtained from getFirehoseData by default and tend to be present across most cancer codes.

Usage

getSubtypeMap(multiassayexperiment)

getClinicalNames(diseaseCode)

splitAssays(multiassayexperiment, sampleCodes = c("01", "11"))

sampleTables(multiassayexperiment, vial = FALSE)

Arguments

multiassayexperiment

A MultiAssayExperiment object

diseaseCode

A TCGA cancer code (e.g., "BRCA")

sampleCodes

A string of sample type codes (refer to data(sampleTypes); default "01", "11")

vial

(logical default FALSE) whether to display vials in the table output

Value

splitAssays

Separates samples by indicated sample codes into different assays in a MultiAssayExperiment. Refer to the sampleTypes data object for a list of available codes. This operation generates n times the number of assays based on the number of sample codes entered. By default, primary solid tumors ("01") and solid tissue normals ("11") are seperated out.

sampleTables

Display all the available samples in each of the assays

Examples

## Not run: 
library(curatedTCGAData)

coad <- curatedTCGAData(diseaseCode = "COAD",
    assays = "CNA*", dry.run = FALSE)
getSubtypeMap(coad)

## End(Not run)

getClinicalNames("COAD")


[Package TCGAutils version 1.2.2 Index]