#test combineList function bsseq
#Noticed it still loads assays into memory after combination
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_BS1
hdf5_BS2 <- BSseq(chr = c("chr1", "chr1", "chr1"),
pos = c(3, 4, 5),
M = hdf5_M,
Cov = hdf5_Cov,
sampleNames = c("D", "E", "F"))
hdf5_BS2
x <- combineList(list(hdf5_BS1, hdf5_BS2), BACKEND = "HDF5Array")
x> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[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] shiny_1.7.4 HDF5Array_1.26.0
[3] DelayedArray_0.24.0 Matrix_1.5-3
[5] plotly_4.10.1 PCAtools_2.10.0
[7] ggrepel_0.9.3 lubridate_1.9.2
[9] forcats_1.0.0 stringr_1.5.0
[11] dplyr_1.1.1 purrr_1.0.1
[13] readr_2.1.4 tidyr_1.3.0
[15] tibble_3.2.1 ggplot2_3.4.1
[17] tidyverse_2.0.0 MethylResolver_0.1.0
[19] methylSig_1.10.0 here_1.0.1
[21] bsseq_1.34.0 SummarizedExperiment_1.28.0
[23] Biobase_2.58.0 MatrixGenerics_1.10.0
[25] matrixStats_0.63.0 GenomicRanges_1.50.2
[27] GenomeInfoDb_1.34.9 IRanges_2.32.0
[29] S4Vectors_0.36.2 BiocGenerics_0.44.0
[31] rhdf5_2.42.0
loaded via a namespace (and not attached):
[1] snow_0.4-4 plyr_1.8.8
[3] lazyeval_0.2.2 splines_4.2.1
[5] BiocParallel_1.32.6 digest_0.6.31
[7] foreach_1.5.2 htmltools_0.5.5
[9] rsconnect_0.8.29 fansi_1.0.4
[11] magrittr_2.0.3 memoise_2.0.1
[13] BSgenome_1.66.3 ScaledMatrix_1.6.0
[15] doParallel_1.0.17 tzdb_0.3.0
[17] limma_3.54.2 Metrics_0.1.4
[19] Biostrings_2.66.0 R.utils_2.12.2
[21] timechange_0.2.0 colorspace_2.1-0
[23] xfun_0.38 crayon_1.5.2
[25] RCurl_1.98-1.12 jsonlite_1.8.4
[27] iterators_1.0.14 glue_1.6.2
[29] polyclip_1.10-4 gtable_0.3.3
[31] zlibbioc_1.44.0 XVector_0.38.0
[33] BiocSingular_1.14.0 Rhdf5lib_1.20.0
[35] DEoptimR_1.0-11 scales_1.2.1
[37] Rcpp_1.0.10 viridisLite_0.4.1
[39] xtable_1.8-4 DSS_2.46.0
[41] dqrng_0.3.0 rsvd_1.0.5
[43] htmlwidgets_1.6.2 httr_1.4.5
[45] ellipsis_0.3.2 varhandle_2.0.5
[47] pkgconfig_2.0.3 XML_3.99-0.14
[49] R.methodsS3_1.8.2 farver_2.1.1
[51] sass_0.4.5 locfit_1.5-9.7
[53] utf8_1.2.3 tidyselect_1.2.0
[55] rlang_1.1.0 reshape2_1.4.4
[57] later_1.3.0 munsell_0.5.0
[59] tools_4.2.1 cachem_1.0.7
[61] cli_3.6.1 generics_0.1.3
[63] fastmap_1.1.1 yaml_2.3.7
[65] knitr_1.42 robustbase_0.95-1
[67] randomForest_4.7-1.1 sparseMatrixStats_1.10.0
[69] mime_0.12 R.oo_1.25.0
[71] compiler_4.2.1 rstudioapi_0.14
[73] tweenr_2.0.2 job_0.3.0
[75] bslib_0.4.2 stringi_1.7.12
[77] lattice_0.20-45 permute_0.9-7
[79] vctrs_0.6.1 trqwe_0.1
[81] pillar_1.9.0 lifecycle_1.0.3
[83] rhdf5filters_1.10.0 jquerylib_0.1.4
[85] data.table_1.14.8 cowplot_1.1.1
[87] bitops_1.0-7 irlba_2.3.5.1
[89] httpuv_1.6.9 rtracklayer_1.58.0
[91] R6_2.5.1 BiocIO_1.8.0
[93] promises_1.2.0.1 codetools_0.2-19
[95] MASS_7.3-58.3 gtools_3.9.4
[97] rprojroot_2.0.3 rjson_0.2.21
[99] withr_2.5.0 GenomicAlignments_1.34.1
[101] Rsamtools_2.14.0 GenomeInfoDbData_1.2.9
[103] parallel_4.2.1 doSNOW_1.0.20
[105] hms_1.1.3 grid_4.2.1
[107] beachmat_2.14.0 DelayedMatrixStats_1.20.0
[109] ggforce_0.4.1 restfulr_0.0.15
When supplying the BACKEND="HDF5Array" as an argument for combineList, the resulting combined object is still loaded in memory.
Here is my output:
> 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
When supplying the BACKEND="HDF5Array" as an argument for combineList, the resulting combined object is still loaded in memory.
Here is my output: