Hi Bhakti, On Mon, Dec 11, 2017 at 12:19 PM, Dwivedi, Bhakti <bhakti.dwiv...@emory.edu> wrote:
> Is there a way to parallelize ConsensusClusterPlus package? > https://bioconductor.org/packages/release/bioc/html/ > ConsensusClusterPlus.html > We are developing a R shiny tool that performs consensus clustering in > addition to other genome-wide analyses. The consensus clustering step is > taking the longest. > Can I do parallel processing in R/R shiny? What parallel package (if any) > I can implement in the R code to do parallel computing? > The canonical package for parallel computing in Bioconductor is BiocParallel: https://bioconductor.org/packages/release/bioc/html/BiocParallel.html One can choose what backend to use for parallelism. You can switch from using SerialParam for cheap and cheerful lapply-like functionality to the default MultiCoreParam and SnowParam which nicely logs useful things like memory usage. It does not look like ConsensusClusterPlus is importing any parallel package of it's own that you need to fight against, so best case scenario is you look at the function of interest you want to run many times and run that function with BiocParallel's bplapply. Or if there are multiple levels of parallelism like internal and external looping then you might have to dive into ConsensusClusterPlus and inject bplapply statements ideally allowing some bpparam() argument passing for the inner and outer loops. > Bhakti > Pariksheet [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
