CODEWITHSUNDEEP
rmatrixmemoryphylogeny
Geomicro
Geomicro

Reputation: 474

memory management for large phylogenetic distance matrix saved as a pd.desc

I'm looking to use iCAMP::bNRI.cm() which requires a phylogenetic distance matrix as an actual matrix. However, my matrix is huge and saved as

new("big.matrix.descriptor", description = list(sharedType = "FileBacked", 
    filename = "pd.bin", dirname = "/dirpath/", 
    totalRows = 5122L, totalCols = 5122L, rowOffset = c(0, 5122
    ), colOffset = c(0, 5122), nrow = 5122, ncol = 5122, rowNames = NULL, 
    colNames = NULL, type = "double", separated = FALSE))

which I can load as a descriptor. How can I specify to iCAMP::bNRI.cm() that my descriptor is the matrix without breaking the memory bank?

bnri.whole <- bNRI.cm(comm=otu, dis=descriptor?, nworker = 4, memo.size.GB = 50...)

Thanks!

Upvotes: 2

Views: 55

Answers (0)

Related Questions