TileDBArray 1.12.0
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 TileDBArray package implements the necessary wrappers around TileDB-R
to support read/write operations on TileDB arrays within the DelayedArray framework.
TileDBArrayCreating a TileDBArray is as easy as:
X <- matrix(rnorm(1000), ncol=10)
library(TileDBArray)
writeTileDBArray(X)## <100 x 10> TileDBMatrix object of type "double":
## [,1] [,2] [,3] ... [,9] [,10]
## [1,] 0.929558309 0.708750712 0.129839139 . -1.4233618 -0.5089131
## [2,] -0.330073990 -0.004954285 -0.897382562 . 0.1480774 -1.5188298
## [3,] 1.277900056 -2.182809214 0.810853572 . -0.1299423 -1.0009916
## [4,] 0.378528881 1.245569941 0.628655059 . -1.0941735 0.1916714
## [5,] -1.106048251 0.426457456 0.908533227 . 0.3022614 0.7996078
## ... . . . . . .
## [96,] -1.36966047 -0.58822976 -0.30957282 . 0.5297854 1.0339910
## [97,] -2.21072003 1.39651195 -0.07258274 . 1.0293996 0.8019768
## [98,] -0.69860623 -0.61462320 -0.72082249 . -0.9296716 -1.6808507
## [99,] 1.64174971 -1.10833100 -2.16041507 . 0.7794137 0.1662348
## [100,] 1.79358187 -0.63200737 -0.60942013 . 0.1944432 0.1266513Alternatively, we can use coercion methods:
as(X, "TileDBArray")## <100 x 10> TileDBMatrix object of type "double":
## [,1] [,2] [,3] ... [,9] [,10]
## [1,] 0.929558309 0.708750712 0.129839139 . -1.4233618 -0.5089131
## [2,] -0.330073990 -0.004954285 -0.897382562 . 0.1480774 -1.5188298
## [3,] 1.277900056 -2.182809214 0.810853572 . -0.1299423 -1.0009916
## [4,] 0.378528881 1.245569941 0.628655059 . -1.0941735 0.1916714
## [5,] -1.106048251 0.426457456 0.908533227 . 0.3022614 0.7996078
## ... . . . . . .
## [96,] -1.36966047 -0.58822976 -0.30957282 . 0.5297854 1.0339910
## [97,] -2.21072003 1.39651195 -0.07258274 . 1.0293996 0.8019768
## [98,] -0.69860623 -0.61462320 -0.72082249 . -0.9296716 -1.6808507
## [99,] 1.64174971 -1.10833100 -2.16041507 . 0.7794137 0.1662348
## [100,] 1.79358187 -0.63200737 -0.60942013 . 0.1944432 0.1266513This process works also for sparse matrices:
Y <- Matrix::rsparsematrix(1000, 1000, density=0.01)
writeTileDBArray(Y)## <1000 x 1000> sparse TileDBMatrix object of type "double":
## [,1] [,2] [,3] ... [,999] [,1000]
## [1,] 0 0 0 . 0.00 0.00
## [2,] 0 0 0 . 0.00 0.00
## [3,] 0 0 0 . 0.00 0.00
## [4,] 0 0 0 . 0.00 0.00
## [5,] 0 0 0 . 0.17 0.00
## ... . . . . . .
## [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 0Logical and integer matrices are supported:
writeTileDBArray(Y > 0)## <1000 x 1000> sparse TileDBMatrix object of type "logical":
## [,1] [,2] [,3] ... [,999] [,1000]
## [1,] FALSE FALSE FALSE . FALSE FALSE
## [2,] FALSE FALSE FALSE . FALSE FALSE
## [3,] FALSE FALSE FALSE . FALSE FALSE
## [4,] FALSE FALSE FALSE . FALSE FALSE
## [5,] FALSE FALSE FALSE . TRUE FALSE
## ... . . . . . .
## [996,] FALSE FALSE FALSE . FALSE FALSE
## [997,] FALSE FALSE FALSE . FALSE FALSE
## [998,] FALSE FALSE FALSE . FALSE FALSE
## [999,] FALSE FALSE FALSE . FALSE FALSE
## [1000,] FALSE FALSE FALSE . FALSE FALSEAs 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)## <100 x 10> TileDBMatrix object of type "double":
## SAMP_1 SAMP_2 SAMP_3 ... SAMP_9 SAMP_10
## GENE_1 0.929558309 0.708750712 0.129839139 . -1.4233618 -0.5089131
## GENE_2 -0.330073990 -0.004954285 -0.897382562 . 0.1480774 -1.5188298
## GENE_3 1.277900056 -2.182809214 0.810853572 . -0.1299423 -1.0009916
## GENE_4 0.378528881 1.245569941 0.628655059 . -1.0941735 0.1916714
## GENE_5 -1.106048251 0.426457456 0.908533227 . 0.3022614 0.7996078
## ... . . . . . .
## GENE_96 -1.36966047 -0.58822976 -0.30957282 . 0.5297854 1.0339910
## GENE_97 -2.21072003 1.39651195 -0.07258274 . 1.0293996 0.8019768
## GENE_98 -0.69860623 -0.61462320 -0.72082249 . -0.9296716 -1.6808507
## GENE_99 1.64174971 -1.10833100 -2.16041507 . 0.7794137 0.1662348
## GENE_100 1.79358187 -0.63200737 -0.60942013 . 0.1944432 0.1266513TileDBArraysTileDBArrays 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)## [1] 100 10head(rownames(out))## [1] "GENE_1" "GENE_2" "GENE_3" "GENE_4" "GENE_5" "GENE_6"head(out[,1])## GENE_1 GENE_2 GENE_3 GENE_4 GENE_5 GENE_6
## 0.9295583 -0.3300740 1.2779001 0.3785289 -1.1060483 0.5542262We 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] ## <5 x 5> DelayedMatrix object of type "double":
## SAMP_1 SAMP_2 SAMP_3 SAMP_4 SAMP_5
## GENE_1 0.929558309 0.708750712 0.129839139 -1.732498856 -0.441560405
## GENE_2 -0.330073990 -0.004954285 -0.897382562 -0.848580979 1.467152348
## GENE_3 1.277900056 -2.182809214 0.810853572 0.992073694 0.864299543
## GENE_4 0.378528881 1.245569941 0.628655059 2.210148108 -0.067710818
## GENE_5 -1.106048251 0.426457456 0.908533227 -0.939379261 0.486224190out * 2## <100 x 10> DelayedMatrix object of type "double":
## SAMP_1 SAMP_2 SAMP_3 ... SAMP_9 SAMP_10
## GENE_1 1.859116617 1.417501425 0.259678279 . -2.8467235 -1.0178263
## GENE_2 -0.660147980 -0.009908571 -1.794765125 . 0.2961548 -3.0376596
## GENE_3 2.555800113 -4.365618429 1.621707145 . -0.2598846 -2.0019833
## GENE_4 0.757057763 2.491139881 1.257310118 . -2.1883470 0.3833428
## GENE_5 -2.212096502 0.852914912 1.817066454 . 0.6045228 1.5992156
## ... . . . . . .
## GENE_96 -2.7393209 -1.1764595 -0.6191456 . 1.0595708 2.0679820
## GENE_97 -4.4214401 2.7930239 -0.1451655 . 2.0587993 1.6039536
## GENE_98 -1.3972125 -1.2292464 -1.4416450 . -1.8593431 -3.3617014
## GENE_99 3.2834994 -2.2166620 -4.3208301 . 1.5588275 0.3324697
## GENE_100 3.5871637 -1.2640147 -1.2188403 . 0.3888864 0.2533026We can also do more complex matrix operations that are supported by DelayedArray:
colSums(out)## SAMP_1 SAMP_2 SAMP_3 SAMP_4 SAMP_5 SAMP_6 SAMP_7
## -5.7026963 -0.4681445 1.6300003 18.9307014 6.8542918 3.7101758 2.2767689
## SAMP_8 SAMP_9 SAMP_10
## -3.2228711 0.5993411 -4.9288266out %*% runif(ncol(out))## <100 x 1> DelayedMatrix object of type "double":
## y
## GENE_1 0.3393299
## GENE_2 0.1624330
## GENE_3 1.4314493
## GENE_4 2.6782522
## GENE_5 -0.1515377
## ... .
## GENE_96 -1.2643402
## GENE_97 2.0813893
## GENE_98 -0.5008821
## GENE_99 -0.9803960
## GENE_100 2.5481826We 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")## <100 x 10> TileDBMatrix object of type "double":
## [,1] [,2] [,3] ... [,9] [,10]
## [1,] -1.160527647 2.721774203 -0.378241384 . 0.15203287 -0.63644596
## [2,] 0.878587396 -0.997936216 0.725517131 . -0.08073936 -0.22325749
## [3,] 1.349267131 0.726267819 -0.004527957 . -0.24787455 0.80861855
## [4,] 0.527563793 0.235495643 0.797130187 . -0.22757613 -1.19722246
## [5,] -0.107688189 -0.100832789 1.186051322 . -0.26265585 -1.10890469
## ... . . . . . .
## [96,] 2.1658066 -0.4625497 -0.5238744 . 1.21220096 -0.66602999
## [97,] 0.3822704 -1.7331442 0.8078355 . -0.05236811 0.57188141
## [98,] -1.0765114 0.3610272 -0.6542989 . -0.56628450 -1.08775994
## [99,] -0.7896832 1.8521445 1.2013592 . -0.89275899 0.98626253
## [100,] 0.6839981 0.6419564 -0.4801739 . 1.34689220 -0.03361355As 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.## <100 x 10> TileDBMatrix object of type "double":
## [,1] [,2] [,3] ... [,9] [,10]
## [1,] -1.160527647 2.721774203 -0.378241384 . 0.15203287 -0.63644596
## [2,] 0.878587396 -0.997936216 0.725517131 . -0.08073936 -0.22325749
## [3,] 1.349267131 0.726267819 -0.004527957 . -0.24787455 0.80861855
## [4,] 0.527563793 0.235495643 0.797130187 . -0.22757613 -1.19722246
## [5,] -0.107688189 -0.100832789 1.186051322 . -0.26265585 -1.10890469
## ... . . . . . .
## [96,] 2.1658066 -0.4625497 -0.5238744 . 1.21220096 -0.66602999
## [97,] 0.3822704 -1.7331442 0.8078355 . -0.05236811 0.57188141
## [98,] -1.0765114 0.3610272 -0.6542989 . -0.56628450 -1.08775994
## [99,] -0.7896832 1.8521445 1.2013592 . -0.89275899 0.98626253
## [100,] 0.6839981 0.6419564 -0.4801739 . 1.34689220 -0.03361355sessionInfo()## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] RcppSpdlog_0.0.14 TileDBArray_1.12.0 DelayedArray_0.28.0
## [4] SparseArray_1.2.0 S4Arrays_1.2.0 abind_1.4-5
## [7] IRanges_2.36.0 S4Vectors_0.40.0 MatrixGenerics_1.14.0
## [10] matrixStats_1.0.0 BiocGenerics_0.48.0 Matrix_1.6-1.1
## [13] BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] bit_4.0.5 jsonlite_1.8.7 compiler_4.3.1
## [4] BiocManager_1.30.22 crayon_1.5.2 Rcpp_1.0.11
## [7] jquerylib_0.1.4 yaml_2.3.7 fastmap_1.1.1
## [10] lattice_0.22-5 R6_2.5.1 RcppCCTZ_0.2.12
## [13] XVector_0.42.0 tiledb_0.21.1 knitr_1.44
## [16] bookdown_0.36 bslib_0.5.1 rlang_1.1.1
## [19] cachem_1.0.8 xfun_0.40 sass_0.4.7
## [22] bit64_4.0.5 cli_3.6.1 zlibbioc_1.48.0
## [25] spdl_0.0.5 digest_0.6.33 grid_4.3.1
## [28] data.table_1.14.8 evaluate_0.22 nanotime_0.3.7
## [31] zoo_1.8-12 rmarkdown_2.25 tools_4.3.1
## [34] htmltools_0.5.6.1