qreduceTCGA {TCGAutils} | R Documentation |
Simplify curatedTCGAData objects by replacing RaggedExperiment objects
qreduceTCGA(obj, keep = FALSE, suffix = "_simplified")
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. |
Relies on TxDb.Hsapiens.UCSC.hg19.knownGene and org.Hs.eg.db to map to hg19 NCBI build.
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.
L. Waldron
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)