curatedTCGAData-helpers: Helper functions for managing MultiAssayExperiment from...

In TCGAutils: TCGA utility functions for data management

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 = NULL, exclusive = FALSE)

sampleTables(multiassayexperiment, vial = FALSE)

Arguments

multiassayexperiment	A MultiAssayExperiment object
diseaseCode	A TCGA cancer code (e.g., "BRCA")
sampleCodes	character (default NULL) A string of sample type codes (refer to data(sampleTypes); splitAssays section)
exclusive	logical (default FALSE) Whether to return only assays that contain all codes in 'sampleCodes'
vial	(logical default FALSE) whether to display vials in the table output

Value

• getSubtypeMap: A data.frame with columns representing actual data variables and explanatory names

• getClinicalNames: A vector of names that correspond to a particular disease code.

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, all assays will be split by samples present in the data.

sampleTables

Display all the available samples in each of the assays

Examples

library(curatedTCGAData)

gbm <- curatedTCGAData("GBM", c("RPPA*", "CNA*"), FALSE)

getSubtypeMap(gbm)

getClinicalNames("COAD")

TCGAutils documentation built on April 17, 2021, 6:04 p.m.