The alabaster.matrix package implements methods for saving and loading matrix- or array-like objects under the alabaster framework. It provides a language-agnostic method for serializing data in arrays or abstractions thereof. To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.matrix")
We can then save a variety of matrices and arrays to file. For example, a sparse matrix can be saved to a HDF5 file in compressed sparse column format:
library(Matrix) y <- rsparsematrix(1000, 100, density=0.05) # Saving it to a directory. library(alabaster.matrix) tmp <- tempfile() saveObject(y, tmp) # Reading it as a file-backed matrix. roundtrip <- readObject(tmp) roundtrip ## <1000 x 100> sparse ReloadedMatrix object of type "double": ## [,1] [,2] [,3] ... [,99] [,100] ## [1,] 0 0 0 . 0 0 ## [2,] 0 0 0 . 0 0 ## [3,] 0 0 0 . 0 0 ## [4,] 0 0 0 . 0 0 ## [5,] 0 0 0 . 0 0 ## ... . . . . . . ## [996,] 0 0 0 . 0 0 ## [997,] 0 0 0 . 0 0 ## [998,] 0 0 0 . 0 0 ## [999,] 0 0 0 . 0 0 ## [1000,] 0 0 0 . 0 0 # Coerce this back into an in-memory sparse matrix: inmemory <- as(roundtrip, "dgCMatrix")
We can also handle DelayedArray objects, possibly with preservation of delayed operations. This uses the chihaya specification to represent delayed operations inside a HDF5 file.
library(DelayedArray) y <- DelayedArray(rsparsematrix(1000, 100, 0.05)) y <- log1p(abs(y) / 1:100) # adding some delayed ops. # Default method saves without preserving delayed operations. tmp <- tempfile() saveObject(y, tmp) readObjectFile(tmp)$type ## [1] "compressed_sparse_matrix" # But we can enable the delayed'ness explicitly, if so desired. tmp2 <- tempfile() saveObject(y, tmp2, delayedarray.preserve.ops=TRUE) readObjectFile(tmp2)$type ## [1] "delayed_array" roundtrip <- readObject(tmp2) roundtrip ## <1000 x 100> sparse ReloadedMatrix object of type "double": ## [,1] [,2] [,3] ... [,99] [,100] ## [1,] 0 0 0 . 0 0 ## [2,] 0 0 0 . 0 0 ## [3,] 0 0 0 . 0 0 ## [4,] 0 0 0 . 0 0 ## [5,] 0 0 0 . 0 0 ## ... . . . . . . ## [996,] 0 0 0 . 0.000000000 0.007368618 ## [997,] 0 0 0 . 0.000000000 0.000000000 ## [998,] 0 0 0 . 0.000000000 0.000000000 ## [999,] 0 0 0 . 0.000000000 0.000000000 ## [1000,] 0 0 0 . 0.000000000 0.000000000
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