GDSArray: Representing GDS files as array-like objects (original) (raw)
Introduction
GDSArray is a Bioconductor package that represents GDS files as objects derived from the DelayedArray package and DelayedArrayclass. It converts a GDS node in the file to a DelayedArray-derived data structure. The rich common methods and data operations defined onGDSArray makes it more _R_-user-friendly than working with the GDS file directly.
Package installation
- Download the package from Bioconductor.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GDSArray")- Load the package into R session.
library(GDSArray)GDS format introduction
Genomic Data Structure (GDS)
The Bioconductor package gdsfmt has provided a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which is designed for large-scale datasets, especially for data which are much larger than the available random-access memory.
More details about GDS format can be found in the vignettes of thegdsfmt, SNPRelate, and SeqArray packages.
GDSArray, GDSMatrix, and GDSFile
GDSArray represents GDS files as DelayedArray instances. It has methods like dim, dimnames defined, and it inherits array-like operations and methods from DelayedArray, e.g., the subsetting method of [.
GDSArray, GDSMatrix, and DelayedArray
The GDSArray() constructor takes as arguments the file path and the GDS node inside the GDS file. The GDSArray() constructor always returns the object with rows being features (genes / variants / snps) and the columns being “samples”. This is consistent with the assay data inside SummarizedExperiment. FIXME: should GDSArray() return that dim?
file <- gdsExampleFileName("seqgds")## This is a SeqArray GDS fileGDSArray(file, "genotype/data")## <2 x 90 x 1348> GDSArray object of type "integer":
## ,,1
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 3 3 0 3 . 0 0 0 0
## [2,] 3 3 0 3 . 0 0 0 0
##
## ,,2
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 3 3 0 3 . 0 0 0 0
## [2,] 3 3 0 3 . 0 0 0 0
##
## ...
##
## ,,1347
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 0 0 0 0 . 0 0 0 0
## [2,] 0 0 0 0 . 0 0 0 0
##
## ,,1348
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 3 3 0 3 . 3 3 3 3
## [2,] 3 3 1 3 . 3 3 3 3A GDSMatrix is a 2-dimensional GDSArray, and will be returned from the GDSArray() constructor automatically if the input GDS node is 2-dimensional.
GDSArray(file, "annotation/format/DP/data")## <90 x 1348> GDSMatrix object of type "integer":
## [,1] [,2] [,3] [,4] ... [,1345] [,1346] [,1347] [,1348]
## [1,] 0 0 12 15 . 6 5 4 0
## [2,] 0 0 17 4 . 10 8 7 0
## [3,] 107 92 247 177 . 28 15 26 3
## ... . . . . . . . . .
## [88,] 81 84 217 110 . 36 61 92 0
## [89,] 67 47 134 111 . 46 57 71 2
## [90,] 156 150 417 195 . 78 101 144 2GDSFile
The GDSFile is a light-weight class to represent GDS files. It has the $ completion method to complete any possible gds nodes. It could be used as a convenient GDSArray constructor if the slot ofcurrent_path in GDSFile object represents a valid gds node. Otherwise, it will return the GDSFile object with an updatedcurrent_path.
gf <- GDSFile(file)
gf$annotation$info## class: GDSFile
## file: /home/biocbuild/bbs-3.22-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds
## current node: annotation/info
## subnodes:
## annotation/info/AA
## annotation/info/AC
## annotation/info/AN
## annotation/info/DP
## annotation/info/HM2
## annotation/info/HM3
## annotation/info/OR
## annotation/info/GP
## annotation/info/BNgf$annotation$info$AC## <1348> GDSArray object of type "integer":
## [1] [2] [3] [4] . [1345] [1346] [1347] [1348]
## 4 1 6 128 . 2 11 1 1Try typing in gf$ann and pressing tab key for the completion.
GDSArray methods
slot accessors.
seedreturns theGDSArraySeedof theGDSArrayobject.
gt <- GDSArray(file, "genotype/data")
seed(gt)## GDSArraySeed
## GDS File path: /home/biocbuild/bbs-3.22-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds
## Array node: genotype/data
## Dim: 2 x 90 x 1348gdsfilereturns the file path of the corresponding GDS file.
gdsfile(gt)## [1] "/home/biocbuild/bbs-3.22-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds"Available GDS nodes
gdsnodes() takes the GDS file path or GDSFile object as input, and returns all nodes that can be converted to GDSArray instances. The returned GDS node names can be used as input for the GDSArray(name=)constructor.
gdsnodes(file)## [1] "sample.id" "variant.id"
## [3] "position" "chromosome"
## [5] "allele" "genotype/data"
## [7] "genotype/~data" "genotype/extra.index"
## [9] "genotype/extra" "phase/data"
## [11] "phase/~data" "phase/extra.index"
## [13] "phase/extra" "annotation/id"
## [15] "annotation/qual" "annotation/filter"
## [17] "annotation/info/AA" "annotation/info/AC"
## [19] "annotation/info/AN" "annotation/info/DP"
## [21] "annotation/info/HM2" "annotation/info/HM3"
## [23] "annotation/info/OR" "annotation/info/GP"
## [25] "annotation/info/BN" "annotation/format/DP/data"
## [27] "annotation/format/DP/~data" "sample.annotation/family"identical(gdsnodes(file), gdsnodes(gf))## [1] TRUEvarname <- gdsnodes(file)[2]
GDSArray(file, varname)## <1348> GDSArray object of type "integer":
## [1] [2] [3] [4] . [1345] [1346] [1347] [1348]
## 1 2 3 4 . 1345 1346 1347 1348dim(), dimnames()
The dimnames(GDSArray) returns an unnamed list, with the value of NULL or dimension names with length being the same as return fromdim(GDSArray).
dp <- GDSArray(file, "annotation/format/DP/data")
dim(dp)## [1] 90 1348class(dimnames(dp))## [1] "list"lengths(dimnames(dp))## [1] 0 0[ subsetting
GDSArray instances can be subset, following the usual _R_conventions, with numeric or logical vectors; logical vectors are recycled to the appropriate length.
dp[1:3, 10:15]## <3 x 6> DelayedMatrix object of type "integer":
## [,1] [,2] [,3] [,4] [,5] [,6]
## [1,] 59 49 88 55 46 47
## [2,] 33 22 16 9 7 7
## [3,] 276 271 145 89 70 151dp[c(TRUE, FALSE), ]## <45 x 1348> DelayedMatrix object of type "integer":
## [,1] [,2] [,3] [,4] ... [,1345] [,1346] [,1347] [,1348]
## [1,] 0 0 12 15 . 6 5 4 0
## [2,] 107 92 247 177 . 28 15 26 3
## [3,] 0 0 17 0 . 4 4 4 0
## ... . . . . . . . . .
## [43,] 0 0 11 5 . 3 3 1 0
## [44,] 3 4 9 2 . 4 3 4 0
## [45,] 67 47 134 111 . 46 57 71 2some numeric calculation
log(dp)## <90 x 1348> DelayedMatrix object of type "double":
## [,1] [,2] [,3] ... [,1347] [,1348]
## [1,] -Inf -Inf 2.484907 . 1.386294 -Inf
## [2,] -Inf -Inf 2.833213 . 1.945910 -Inf
## [3,] 4.672829 4.521789 5.509388 . 3.258097 1.098612
## ... . . . . . .
## [88,] 4.394449 4.430817 5.379897 . 4.5217886 -Inf
## [89,] 4.204693 3.850148 4.897840 . 4.2626799 0.6931472
## [90,] 5.049856 5.010635 6.033086 . 4.9698133 0.6931472dp[rowMeans(dp) < 60, ]## <52 x 1348> DelayedMatrix object of type "integer":
## [,1] [,2] [,3] [,4] ... [,1345] [,1346] [,1347] [,1348]
## [1,] 0 0 12 15 . 6 5 4 0
## [2,] 0 0 17 4 . 10 8 7 0
## [3,] 0 0 11 1 . 3 1 1 0
## ... . . . . . . . . .
## [50,] 0 0 6 0 . 2 0 0 0
## [51,] 0 0 11 5 . 3 3 1 0
## [52,] 3 4 9 2 . 4 3 4 0Internals: GDSArraySeed
The GDSArraySeed class represents the ‘seed’ for the GDSArrayobject. It is not exported from the GDSArray package. Seed objects should contain the GDS file path, node name, and are expected to satisfy the seed contractfor implementing a DelayedArray backend, i.e. to support dim() and dimnames().
seed <- GDSArray:::GDSArraySeed(file, "genotype/data")
seed## GDSArraySeed
## GDS File path: /home/biocbuild/bbs-3.22-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds
## Array node: genotype/data
## Dim: 2 x 90 x 1348The seed can be used to construct a GDSArray instance.
GDSArray(seed)## <2 x 90 x 1348> GDSArray object of type "integer":
## ,,1
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 3 3 0 3 . 0 0 0 0
## [2,] 3 3 0 3 . 0 0 0 0
##
## ,,2
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 3 3 0 3 . 0 0 0 0
## [2,] 3 3 0 3 . 0 0 0 0
##
## ...
##
## ,,1347
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 0 0 0 0 . 0 0 0 0
## [2,] 0 0 0 0 . 0 0 0 0
##
## ,,1348
## [,1] [,2] [,3] [,4] ... [,87] [,88] [,89] [,90]
## [1,] 3 3 0 3 . 3 3 3 3
## [2,] 3 3 1 3 . 3 3 3 3The DelayedArray() constructor with GDSArraySeed object as argument will return the same content as the GDSArray() constructor over the same GDSArraySeed.
class(DelayedArray(seed))## [1] "GDSArray"
## attr(,"package")
## [1] "GDSArray"sessionInfo
sessionInfo()## R version 4.5.0 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## 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] GDSArray_1.29.0 DelayedArray_0.35.0 SparseArray_1.9.0
## [4] S4Arrays_1.9.0 abind_1.4-8 IRanges_2.43.0
## [7] S4Vectors_0.47.0 MatrixGenerics_1.21.0 matrixStats_1.5.0
## [10] Matrix_1.7-3 BiocGenerics_0.55.0 generics_0.1.3
## [13] gdsfmt_1.45.0 BiocStyle_2.37.0
##
## loaded via a namespace (and not attached):
## [1] jsonlite_2.0.0 compiler_4.5.0 BiocManager_1.30.25
## [4] crayon_1.5.3 Biostrings_2.77.0 GenomicRanges_1.61.0
## [7] parallel_4.5.0 jquerylib_0.1.4 yaml_2.3.10
## [10] fastmap_1.2.0 lattice_0.22-7 R6_2.6.1
## [13] XVector_0.49.0 GenomeInfoDb_1.45.0 knitr_1.50
## [16] bookdown_0.43 GenomeInfoDbData_1.2.14 bslib_0.9.0
## [19] rlang_1.1.6 cachem_1.1.0 xfun_0.52
## [22] sass_0.4.10 cli_3.6.4 digest_0.6.37
## [25] grid_4.5.0 SeqArray_1.49.0 lifecycle_1.0.4
## [28] evaluate_1.0.3 httr_1.4.7 rmarkdown_2.29
## [31] tools_4.5.0 htmltools_0.5.8.1 UCSC.utils_1.5.0