qreduceTCGA {TCGAutils}R Documentation

Simplify curatedTCGAData objects by replacing RaggedExperiment objects

Description

Simplify curatedTCGAData objects by replacing RaggedExperiment objects

Usage

qreduceTCGA(obj, keep = FALSE, suffix = "_simplified")

Arguments

obj

A MultiAssayExperiment object obtained from curatedTCGAData

keep

logical (default FALSE) whether to remove the original RaggedExperiment objects from the returned MultiAssayExperiment

suffix

character (default "_simplified") A character string to append to the newly modified assay.

Details

Relies on TxDb.Hsapiens.UCSC.hg19.knownGene and org.Hs.eg.db to map to hg19 NCBI build.

Value

A MultiAssayExperiment object with RaggedExperiments converted to RangedSummarizedExperiment with rows corresponding to gene symbol.

"Mutations" objects become a genes x patients RangedSummarizedExperiment containing 1 if there is a non-silent mutation somewhere in the gene, and 0 otherwise. "CNA" and "CNV" segmented copy number are reduced using a weighted mean in the rare cases of overlapping (non-disjoint) copy number regions.

Author(s)

L. Waldron

Examples

library(curatedTCGAData)
library(GenomeInfoDb)

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

## Update build to "hg19"
genome(accmae[["ACC_Mutation-20160128"]]) <-
    vapply(genome(accmae[["ACC_Mutation-20160128"]]),
    translateBuild, character(1L))

qreduceTCGA(accmae)


[Package TCGAutils version 1.2.2 Index]