GSVA consumes much RAM

[ivokwee]

GSVA consumes much RAM

[ivokwee]

Using the peakRAM package, I got a peak RAM usage of 1470Mb (1.5Gb) using the example data and example playdata::GSETS. It would be good to test other memory profiling methods. Not sure is peakRAM is the correct way or best.

if(0) {
  BiocManager::install("GSVA",force=TRUE)
  remotes::install_github("rcastelo/GSVA")
  remotes::install_version("matrixStats", version="1.1.0")
  install.packages("peakRAM")
}

counts <- playbase::COUNTS
X <- playbase::logCPM(counts + 1)
geneSets <- playdata::GSETS
length(geneSets)
## 123832

gsvapar <- GSVA::gsvaParam(X, geneSets, maxDiff=TRUE)
mem <- peakRAM::peakRAM({res <- GSVA::gsva(gsvapar)})
mem
## 1489.3 MiB  105.508sec

gsvapar <- GSVA::ssgseaParam(X, geneSets)
mem <- peakRAM::peakRAM({res <- GSVA::gsva(gsvapar)})
mem
## 1470.3 MiB  366.266sec