GDSArray 1.14.1
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.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GDSArray")library(GDSArray)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.
GDSArray, GDSMatrix, and GDSFileGDSArray 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 [.
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> array of class GDSArray and 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> matrix of class GDSMatrix and 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 2GDSFileThe 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-3.14-bioc/R/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$AC## <1348> array of class GDSArray and type "integer":
## [1] [2] [3] [4] . [1345] [1346] [1347] [1348]
## 4 1 6 128 . 2 11 1 1Try typing in gf$ann and pressing tab key for the completion.
GDSArray methodsseed returns the GDSArraySeed of the GDSArray object.gt <- GDSArray(file, "genotype/data")
seed(gt)## GDSArraySeed
## File: /home/biocbuild/bbs-3.14-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
## Array node: genotype/data
## Dim: 2 x 90 x 1348gdsfile returns the file path of the corresponding GDS file.gdsfile(gt)## [1] "/home/biocbuild/bbs-3.14-bioc/R/library/SeqArray/extdata/CEU_Exon.gds"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> array of class GDSArray and 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 from
dim(GDSArray).
dp <- GDSArray(file, "annotation/format/DP/data")
dim(dp)## [1] 90 1348class(dimnames(dp))## [1] "list"lengths(dimnames(dp))## [1] 0 0[ subsettingGDSArray 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> matrix of class DelayedMatrix and 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> matrix of class DelayedMatrix and 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 2log(dp)## <90 x 1348> matrix of class DelayedMatrix and 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> matrix of class DelayedMatrix and 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 0GDSArraySeedThe GDSArraySeed class represents the ‘seed’ for the GDSArray
object. It is not exported from the GDSArray package. Seed objects
should contain the gds file of gds.class, GDS file path, GDS file
node name, and are expected to satisfy the seed
contract
for implementing a DelayedArray backend, i.e. to support dim() and
dimnames().
gds <- openfn.gds(file)
seed <- GDSArray:::GDSArraySeed(gds, "genotype/data")
seed## GDSArraySeed
## File: /home/biocbuild/bbs-3.14-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
## Array node: genotype/data
## Dim: 2 x 90 x 1348closefn.gds(gds)The seed can be used to construct a GDSArray instance.
GDSArray(seed)## <2 x 90 x 1348> array of class GDSArray and 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()## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
##
## 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
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] GDSArray_1.14.1 DelayedArray_0.20.0 IRanges_2.28.0
## [4] S4Vectors_0.32.3 MatrixGenerics_1.6.0 matrixStats_0.61.0
## [7] Matrix_1.4-0 BiocGenerics_0.40.0 gdsfmt_1.30.0
## [10] BiocStyle_2.22.0
##
## loaded via a namespace (and not attached):
## [1] XVector_0.34.0 bslib_0.3.1 compiler_4.1.2
## [4] BiocManager_1.30.16 jquerylib_0.1.4 GenomeInfoDb_1.30.0
## [7] zlibbioc_1.40.0 bitops_1.0-7 tools_4.1.2
## [10] digest_0.6.29 jsonlite_1.7.2 evaluate_0.14
## [13] lattice_0.20-45 rlang_0.4.12 SeqArray_1.34.0
## [16] yaml_2.2.1 parallel_4.1.2 xfun_0.29
## [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 stringr_1.4.0
## [22] knitr_1.37 Biostrings_2.62.0 sass_0.4.0
## [25] grid_4.1.2 R6_2.5.1 rmarkdown_2.11
## [28] bookdown_0.24 magrittr_2.0.1 htmltools_0.5.2
## [31] GenomicRanges_1.46.1 stringi_1.7.6 RCurl_1.98-1.5
## [34] crayon_1.4.2