Comments (1)
PeteHaitch
commented on July 18, 2024
Thanks for your patience while I was on leave.
I can confirm that bsseq::combineList() seems to be ignoring the BACKEND argument in this case.
I'm not sure exactly why and haven't had time to dig into this further.
But a workaround is to call HDF5Array::setAutoRealizationBackend("HDF5Array") before running bsseq::combineList(), as shown in the example below.
suppressPackageStartupMessages(library(bsseq))
suppressPackageStartupMessages(library(HDF5Array))
M <- matrix(0:8, 3, 3)
Cov <- matrix(1:9, 3, 3)
hdf5_M <- writeHDF5Array(M)
hdf5_Cov <- writeHDF5Array(Cov)
hdf5_BS1 <- BSseq(
chr = c("chr1", "chr2", "chr1"),
pos = c(1, 2, 3),
M = hdf5_M,
Cov = hdf5_Cov,
sampleNames = c("A", "B", "C"))
hdf5_BS2 <- BSseq(
chr = c("chr1", "chr1", "chr1"),
pos = c(3, 4, 5),
M = hdf5_M,
Cov = hdf5_Cov,
sampleNames = c("D", "E", "F"))
# Assay is in-memory despite specifying `BACKEND = "HDF5Arra"`
x <- combineList(list(hdf5_BS1, hdf5_BS2), BACKEND = "HDF5Array")
x
#> An object of type 'BSseq' with
#> 5 methylation loci
#> 6 samples
#> has not been smoothed
#> All assays are in-memory
showtree(assay(x))
#> 5x6 integer: DelayedMatrix object
#> └─ 5x6 integer: Set dimnames
#> └─ 5x6 integer: [seed] matrix object
# Assay is on-disk (as expected)
setAutoRealizationBackend("HDF5Array")
y <- combineList(list(hdf5_BS1, hdf5_BS2))
y
#> An object of type 'BSseq' with
#> 5 methylation loci
#> 6 samples
#> has not been smoothed
#> Some assays are HDF5Array-backed
showtree(assay(y))
#> 5x6 integer: DelayedMatrix object
#> └─ 5x6 integer: Set dimnames
#> └─ 5x6 integer: [seed] HDF5ArraySeed objectSession info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R Under development (unstable) (2023-02-13 r83829)
#> os macOS Ventura 13.3.1
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Australia/Melbourne
#> date 2023-05-02
#> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> beachmat 2.17.0 2023-04-25 [1] Bioconductor
#> Biobase * 2.61.0 2023-04-25 [1] Bioconductor
#> BiocGenerics * 0.47.0 2023-04-25 [1] Bioconductor
#> BiocIO 1.11.0 2023-04-25 [1] Bioconductor
#> BiocParallel 1.35.0 2023-04-25 [1] Bioconductor
#> Biostrings 2.69.0 2023-04-25 [1] Bioconductor
#> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
#> BSgenome 1.69.0 2023-04-25 [1] Bioconductor
#> bsseq * 1.37.0 2023-04-25 [1] Bioconductor
#> cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
#> codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.0)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
#> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
#> data.table 1.14.8 2023-02-17 [1] CRAN (R 4.3.0)
#> DelayedArray * 0.27.0 2023-04-25 [1] Bioconductor
#> DelayedMatrixStats 1.23.0 2023-04-25 [1] Bioconductor
#> digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.3.0)
#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
#> fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0)
#> GenomeInfoDb * 1.37.0 2023-04-25 [1] Bioconductor
#> GenomeInfoDbData 1.2.10 2023-03-26 [1] Bioconductor
#> GenomicAlignments 1.37.0 2023-04-25 [1] Bioconductor
#> GenomicRanges * 1.53.0 2023-04-25 [1] Bioconductor
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
#> gtools 3.9.4 2022-11-27 [1] CRAN (R 4.3.0)
#> HDF5Array * 1.29.0 2023-04-25 [1] Bioconductor
#> htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
#> IRanges * 2.35.0 2023-04-25 [1] Bioconductor
#> knitr 1.42 2023-01-25 [1] CRAN (R 4.3.0)
#> lattice 0.21-8 2023-04-05 [1] CRAN (R 4.3.0)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
#> limma 3.57.0 2023-04-25 [1] Bioconductor
#> locfit 1.5-9.7 2023-01-02 [1] CRAN (R 4.3.0)
#> Matrix * 1.5-4 2023-04-04 [1] CRAN (R 4.3.0)
#> MatrixGenerics * 1.13.0 2023-04-25 [1] Bioconductor
#> matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.3.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
#> permute 0.9-7 2022-01-27 [1] CRAN (R 4.3.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0)
#> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
#> Rcpp 1.0.10 2023-01-22 [1] CRAN (R 4.3.0)
#> RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.3.0)
#> restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
#> rhdf5 * 2.45.0 2023-04-25 [1] Bioconductor
#> rhdf5filters 1.13.2 2023-04-30 [1] Bioconductor
#> Rhdf5lib 1.23.0 2023-04-25 [1] Bioconductor
#> rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
#> rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
#> rmarkdown 2.21 2023-03-26 [1] CRAN (R 4.3.0)
#> Rsamtools 2.17.0 2023-04-25 [1] Bioconductor
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0)
#> rtracklayer 1.61.0 2023-04-25 [1] Bioconductor
#> S4Vectors * 0.39.0 2023-04-25 [1] Bioconductor
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
#> sparseMatrixStats 1.13.0 2023-04-25 [1] Bioconductor
#> SummarizedExperiment * 1.31.0 2023-04-25 [1] Bioconductor
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.3.0)
#> xfun 0.39 2023-04-20 [1] CRAN (R 4.3.0)
#> XML 3.99-0.14 2023-03-19 [1] CRAN (R 4.3.0)
#> XVector 0.41.0 2023-04-25 [1] Bioconductor
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
#> zlibbioc 1.47.0 2023-04-25 [1] Bioconductor
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────from bsseq.
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from bsseq.