simplifyTCGA {TCGAutils}R Documentation

All-in-one simplification of curatedTCGAData objects

Description

All-in-one simplification of curatedTCGAData objects

Usage

simplifyTCGA(obj, keep = FALSE)

Arguments

obj

A MultiAssayExperiment from curatedTCGAData

keep

If FALSE (default), remove the original MultiAssayExperiment elements that have simplified versions in the output.

Value

a MultiAssayExperiment with any gene expression, miRNA, copy number, and mutations converted to RangedSummarizedExperiment objects

Author(s)

L. Waldron

See Also

mirToRanges, symbolsToRanges, qreduceTCGA

Examples

library(curatedTCGAData)
library(GenomeInfoDb)

accmae <- curatedTCGAData("ACC",
    c("CNASNP", "Mutation", "miRNASeqGene", "GISTICT"),
    dry.run = FALSE)

rex <- accmae[["ACC_Mutation-20160128"]]

## Translate build to "hg19"
tgenome <- vapply(genome(rex), translateBuild, character(1L))
genome(rex) <- tgenome

accmae[["ACC_Mutation-20160128"]] <- rex

simplifyTCGA(accmae)


[Package TCGAutils version 1.2.2 Index]