simplifyTCGA: All-in-one simplification of curatedTCGAData objects

Description Usage Arguments Value Author(s) See Also Examples

View source: R/simplifyTCGA.R

Description

All-in-one simplification of curatedTCGAData objects

Usage

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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

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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)

waldronlab/BiocInterfaces documentation built on Nov. 16, 2018, 1:19 a.m.