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. The array data from GDS files are always returned with the first dimension being variants/snps and the second dimension being samples. This feature is consistent with the assay data saved in SummarizedExperiment, and makes the GDSArray package interoperable with other established Bioconductor data infrastructure.

2 Package installation

  1. Download the package from Bioconductor.
source("https://bioconductor.org/biocLite.R")
biocLite("GDSArray")
  1. 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.

The GDS format has been widely used in genetic/genomic research for high-throughput genotyping or sequencing data. There are two major classes that extends the gds.class: SNPGDSFileClass suited for genotyping data (e.g., GWAS), and SeqVarGDSClass that are designed specifically for DNA-sequencing data. The file format attribute in each data class is set as SNP_ARRAY and SEQ_ARRAY. There are rich functions written based on these data classes for common data operation and statistical analysis.

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.

file <- SeqArray::seqExampleFileName("gds")
GDSArray(file, "genotype/data")
## <1348 x 90 x 2> 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
##     ...     .     .     .     .   .     .     .     .     .
## [1347,]     0     0     0     0   .     0     0     0     0
## [1348,]     3     3     0     3   .     3     3     3     3
## 
## , , 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,]     0     0     0     0   .     0     0     0     0
## [1348,]     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, "phase/data")
## <1348 x 90> GDSMatrix object of type "integer":
##      NA06984 NA06985 NA06986 NA06989 ... NA12889 NA12890 NA12891 NA12892
##    1       0       0       0       0   .       0       0       0       0
##    2       0       0       0       0   .       0       0       0       0
##    3       0       0       0       0   .       0       0       0       0
##  ...       .       .       .       .   .       .       .       .       .
## 1346       0       0       0       0   .       0       0       0       0
## 1347       0       0       0       0   .       0       0       0       0
## 1348       0       0       0       0   .       0       0       0       0

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: C:/Users/biocbuild/bbs-3.7-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/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.
ga <- GDSArray(file, "genotype/data")
seed(ga)
## GDSArraySeed
## gds file: C:/Users/biocbuild/bbs-3.7-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
## array data: genotype/data
## dim: 1348 x 90 x 2
  • gdsfile returns the file path of the corresponding GDS file.
gdsfile(ga)
## [1] "C:/Users/biocbuild/bbs-3.7-bioc/R/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] "description"                "sample.id"                 
##  [3] "variant.id"                 "position"                  
##  [5] "chromosome"                 "allele"                    
##  [7] "genotype/data"              "genotype/~data"            
##  [9] "genotype/extra.index"       "genotype/extra"            
## [11] "phase/data"                 "phase/~data"               
## [13] "phase/extra.index"          "phase/extra"               
## [15] "annotation/id"              "annotation/qual"           
## [17] "annotation/filter"          "annotation/info/AA"        
## [19] "annotation/info/AC"         "annotation/info/AN"        
## [21] "annotation/info/DP"         "annotation/info/HM2"       
## [23] "annotation/info/HM3"        "annotation/info/OR"        
## [25] "annotation/info/GP"         "annotation/info/BN"        
## [27] "annotation/format/DP/data"  "annotation/format/DP/~data"
## [29] "sample.annotation/family"
identical(gdsnodes(file), gdsnodes(gf))
## [1] FALSE
GDSArray(file, name=gdsnodes(file)[2])
## <90> GDSArray object of type "character":
##   NA06984   NA06985   NA06986   .         NA12891   NA12892 
## "NA06984" "NA06985" "NA06986"         . "NA12891" "NA12892"

4.3.3 dim(), dimnames()

The dimnames(GDSArray) returns an unnamed list, with the length of each element to be the same as return from dim(GDSArray).

ga <- GDSArray(file, "phase/data")
dim(ga)
## [1] 1348   90
class(dimnames(ga))
## [1] "list"
lengths(dimnames(ga))
## variant.id  sample.id 
##       1348         90

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.

ga[1:3, 10:15]
## <3 x 6> DelayedMatrix object of type "integer":
##   NA07346 NA07347 NA07357 NA10847 NA10851 NA11829
## 1       0       0       0       0       0       0
## 2       0       0       0       0       0       0
## 3       0       0       0       0       0       0
ga[c(TRUE, FALSE), ]
## <674 x 90> DelayedMatrix object of type "integer":
##      NA06984 NA06985 NA06986 NA06989 ... NA12889 NA12890 NA12891 NA12892
##    1       0       0       0       0   .       0       0       0       0
##    3       0       0       0       0   .       0       0       0       0
##    5       0       0       0       0   .       0       0       0       0
##  ...       .       .       .       .   .       .       .       .       .
## 1343       0       0       0       0   .       0       0       0       0
## 1345       0       0       0       0   .       0       0       0       0
## 1347       0       0       0       0   .       0       0       0       0

4.3.5 some numeric calculation

dp <- GDSArray(file, "annotation/format/DP/data")
dp
## <1348 x 90> GDSMatrix object of type "integer":
##      NA06984 NA06985 NA06986 NA06989 ... NA12889 NA12890 NA12891 NA12892
##    1       0       0     107       0   .       3      81      67     156
##    2       0       0      92       0   .       4      84      47     150
##    3      12      17     247      11   .       9     217     134     417
##  ...       .       .       .       .   .       .       .       .       .
## 1346       5       8      15       1   .       3      61      57     101
## 1347       4       7      26       1   .       4      92      71     144
## 1348       0       0       3       0   .       0       0       2       2
log(dp)
## <1348 x 90> DelayedMatrix object of type "double":
##       NA06984  NA06985  NA06986 ...   NA12891   NA12892
##    1     -Inf     -Inf 4.672829   .  4.204693  5.049856
##    2     -Inf     -Inf 4.521789   .  3.850148  5.010635
##    3 2.484907 2.833213 5.509388   .  4.897840  6.033086
##  ...        .        .        .   .         .         .
## 1346 1.609438 2.079442 2.708050   . 4.0430513 4.6151205
## 1347 1.386294 1.945910 3.258097   . 4.2626799 4.9698133
## 1348     -Inf     -Inf 1.098612   . 0.6931472 0.6931472
dp[rowMeans(dp) < 60, ]
## <413 x 90> DelayedMatrix object of type "integer":
##      NA06984 NA06985 NA06986 NA06989 ... NA12889 NA12890 NA12891 NA12892
##    1       0       0     107       0   .       3      81      67     156
##    2       0       0      92       0   .       4      84      47     150
##    4      15       4     177       1   .       2     110     111     195
##  ...       .       .       .       .   .       .       .       .       .
## 1346       5       8      15       1   .       3      61      57     101
## 1347       4       7      26       1   .       4      92      71     144
## 1348       0       0       3       0   .       0       0       2       2

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, and are expected to satisfy the “seed contract” i.e. to support dim() and dimnames().

seed <- GDSArray:::GDSArraySeed(file, "genotype/data")
seed
## GDSArraySeed
## gds file: C:/Users/biocbuild/bbs-3.7-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
## array data: genotype/data
## dim: 1348 x 90 x 2

The seed can be used to construct a GDSArray instance.

GDSArray(seed)
## <1348 x 90 x 2> 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
##     ...     .     .     .     .   .     .     .     .     .
## [1347,]     0     0     0     0   .     0     0     0     0
## [1348,]     3     3     0     3   .     3     3     3     3
## 
## , , 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,]     0     0     0     0   .     0     0     0     0
## [1348,]     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 3.5.0 (2018-04-23)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows Server 2012 R2 x64 (build 9600)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=C                          
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
## [1] GDSArray_1.0.0      DelayedArray_0.6.0  BiocParallel_1.14.0
## [4] IRanges_2.14.0      S4Vectors_0.18.0    matrixStats_0.53.1 
## [7] BiocGenerics_0.26.0 gdsfmt_1.16.0       BiocStyle_2.8.0    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.16           XVector_0.20.0         knitr_1.20            
##  [4] magrittr_1.5           zlibbioc_1.26.0        GenomicRanges_1.32.0  
##  [7] GenomeInfoDb_1.16.0    stringr_1.3.0          tools_3.5.0           
## [10] xfun_0.1               SeqArray_1.20.0        htmltools_0.3.6       
## [13] yaml_2.1.18            rprojroot_1.3-2        digest_0.6.15         
## [16] SNPRelate_1.14.0       bookdown_0.7           GenomeInfoDbData_1.1.0
## [19] bitops_1.0-6           RCurl_1.95-4.10        evaluate_0.10.1       
## [22] rmarkdown_1.9          stringi_1.1.7          compiler_3.5.0        
## [25] Biostrings_2.48.0      backports_1.1.2