# GDSArray: Representing GDS files as array-like objects

Qian Liu1, Hervé Pagès2 and Martin Morgan1

1Roswell Park Comprehensive Cancer Center, Buffalo, NY
2Fred Hutchinson Cancer Research Center, Seattle, WA

#### last edit: 3/26/2024

#### Package

GDSArray 1.32.0

# 1 Introduction

GDSArray is a Bioconductor package that represents GDS files as objects derived from the DelayedArray package and `DelayedArray` class. It converts a GDS node in the file to a `DelayedArray`-derived data structure. The rich common methods and data operations defined on `GDSArray` makes it more R-user-friendly than working with the GDS file directly.

# 2 Package installation

1. Download the package from Bioconductor.

    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install("GDSArray")

2. Load the package into R session.

    library(GDSArray)

# 3 GDS format introduction

## 3.1 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 the gdsfmt, SNPRelate, and SeqArray packages.

# 4 `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 `[`.

## 4.1 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 file

    GDSArray(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     3

A `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       2

## 4.2 `GDSFile`

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 of `current_path` in `GDSFile` object represents a valid gds node. Otherwise, it will return the `GDSFile` object with an updated `current_path`.

    gf <- GDSFile(file)
    gf$annotation$info

    ## class: GDSFile
    ## file: /home/biocbuild/bbs-3.23-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/BN

    gf$annotation$info$AC

    ## <1348> GDSArray object of type "integer":
    ##    [1]    [2]    [3]    [4]      . [1345] [1346] [1347] [1348]
    ##      4      1      6    128      .      2     11      1      1

Try typing in `gf$ann` and pressing `tab` key for the completion.

## 4.3 `GDSArray` methods

### 4.3.1 slot accessors.

- `seed` returns the `GDSArraySeed` of the `GDSArray` object.

    gt <- GDSArray(file, "genotype/data")
    seed(gt)

    ## GDSArraySeed
    ## GDS File path: /home/biocbuild/bbs-3.23-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds
    ## Array node: genotype/data
    ## Dim: 2 x 90 x 1348

- `gdsfile` returns the file path of the corresponding GDS file.

    gdsfile(gt)

    ## [1] "/home/biocbuild/bbs-3.23-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds"

### 4.3.2 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] TRUE

    varname <- 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   1348

### 4.3.3 `dim()`, `dimnames()`

The `dimnames(GDSArray)` returns an unnamed list, with the value of NULL or dimension names with length being the same as return from `dim(GDSArray)`.

    dp <- GDSArray(file, "annotation/format/DP/data")
    dim(dp)

    ## [1]   90 1348

    class(dimnames(dp))

    ## [1] "list"

    lengths(dimnames(dp))

    ## [1] 0 0

### 4.3.4 `[` 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  151

    dp[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       2

### 4.3.5 some 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 0.6931472

    dp[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       0

## 4.4 Internals: `GDSArraySeed`

The `GDSArraySeed` class represents the ‘seed’ for the `GDSArray` object. 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 contract for 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-3.23-bioc/R/site-library/SeqArray/extdata/CEU_Exon.gds
    ## Array node: genotype/data
    ## Dim: 2 x 90 x 1348

The 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     3

The `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"

# 5 sessionInfo

    sessionInfo()

    ## R version 4.6.0 RC (2026-04-17 r89917)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.23-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_1.32.0       DelayedArray_0.38.0   SparseArray_1.12.0
    ##  [4] S4Arrays_1.12.0       abind_1.4-8           IRanges_2.46.0
    ##  [7] S4Vectors_0.50.0      MatrixGenerics_1.24.0 matrixStats_1.5.0
    ## [10] Matrix_1.7-5          BiocGenerics_0.58.0   generics_0.1.4
    ## [13] gdsfmt_1.48.0         BiocStyle_2.40.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] jsonlite_2.0.0       crayon_1.5.3         compiler_4.6.0
    ##  [4] BiocManager_1.30.27  GenomicRanges_1.64.0 Biostrings_2.80.0
    ##  [7] parallel_4.6.0       jquerylib_0.1.4      Seqinfo_1.2.0
    ## [10] yaml_2.3.12          fastmap_1.2.0        lattice_0.22-9
    ## [13] R6_2.6.1             XVector_0.52.0       knitr_1.51
    ## [16] bookdown_0.46        bslib_0.10.0         rlang_1.2.0
    ## [19] cachem_1.1.0         xfun_0.57            sass_0.4.10
    ## [22] otel_0.2.0           cli_3.6.6            digest_0.6.39
    ## [25] grid_4.6.0           SeqArray_1.52.0      lifecycle_1.0.5
    ## [28] evaluate_1.0.5       rmarkdown_2.31       tools_4.6.0
    ## [31] htmltools_0.5.9