GMQL use case (from Masseroli et al 2018, Bioinformatics bty688)

GMQLusecase

# Masseroli et al 2018, https://doi.org/10.1093/bioinformatics/bty688
# "In TCGA data of BRCA patients, find the DNA somatic mutations 
# within the first 2000 bp outside of the genes that are both 
# expressed with FPKM > 3 and have at least a methylation in the same patient
# biospecimen, and extract these mutations of the top 5% patients
# with the highest number of such mutations."

library(curatedTCGAData)
system.time(mae <- curatedTCGAData("ACC", c("Mutation", "RNASeq2GeneNorm", "Methylation"), dry.run = FALSE))

library(TCGAutils)
system.time(mae <- symbolsToRanges(mae))

rangedMethylation <- function(SE){
  SEranged <- SE[!is.na(rowData(SE)$Chromosome), ]
  rd <- rowData(SEranged)
  rowRanges(SEranged) <- GRanges(rd$Chromosome, rd$Genomic_Coordinate)
  genome(SEranged)
  return(SEranged)
}

system.time(mae[[1]] <- rangedMethylation(mae[[1]]))

system.time(mae <- intersectColumns(mae))

Hi Levi, @lwaldron
I've added the rowRanges<- replace method for this function to work in Bioc-devel.
-MR