knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) library(BiocStyle)
TileDB implements a framework for local and remote storage of dense and sparse arrays.
We can use this as a DelayedArray
backend to provide an array-level abstraction,
thus allowing the data to be used in many places where an ordinary array or matrix might be used.
The r Biocpkg("TileDBArray")
package implements the necessary wrappers around r Githubpkg("TileDB-Inc/TileDB-R")
to support read/write operations on TileDB arrays within the r Biocpkg("DelayedArray")
framework.
TileDBArray
Creating a TileDBArray
is as easy as:
X <- matrix(rnorm(1000), ncol=10) library(TileDBArray) writeTileDBArray(X)
Alternatively, we can use coercion methods:
as(X, "TileDBArray")
This process works also for sparse matrices:
Y <- Matrix::rsparsematrix(1000, 1000, density=0.01) writeTileDBArray(Y)
Logical and integer matrices are supported:
writeTileDBArray(Y > 0)
As are matrices with dimension names:
rownames(X) <- sprintf("GENE_%i", seq_len(nrow(X))) colnames(X) <- sprintf("SAMP_%i", seq_len(ncol(X))) writeTileDBArray(X)
TileDBArray
sTileDBArray
s are simply DelayedArray
objects and can be manipulated as such.
The usual conventions for extracting data from matrix-like objects work as expected:
out <- as(X, "TileDBArray") dim(out) head(rownames(out)) head(out[,1])
We can also perform manipulations like subsetting and arithmetic.
Note that these operations do not affect the data in the TileDB backend;
rather, they are delayed until the values are explicitly required,
hence the creation of the DelayedMatrix
object.
out[1:5,1:5] out * 2
We can also do more complex matrix operations that are supported by r Biocpkg("DelayedArray")
:
colSums(out) out %*% runif(ncol(out))
We can adjust some parameters for creating the backend with appropriate arguments to writeTileDBArray()
.
For example, the example below allows us to control the path to the backend
as well as the name of the attribute containing the data.
X <- matrix(rnorm(1000), ncol=10) path <- tempfile() writeTileDBArray(X, path=path, attr="WHEE")
As these arguments cannot be passed during coercion, we instead provide global variables that can be set or unset to affect the outcome.
path2 <- tempfile() setTileDBPath(path2) as(X, "TileDBArray") # uses path2 to store the backend.
sessionInfo()
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