simplifyTCGA {TCGAutils} | R Documentation |
All-in-one simplification of curatedTCGAData objects
simplifyTCGA(obj, keep = FALSE)
obj |
A MultiAssayExperiment from curatedTCGAData |
keep |
If FALSE (default), remove the original MultiAssayExperiment elements that have simplified versions in the output. |
a MultiAssayExperiment with any gene expression, miRNA, copy number, and mutations converted to RangedSummarizedExperiment objects
L. Waldron
mirToRanges, symbolsToRanges, qreduceTCGA
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)