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TENxIO
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- Repository: https://github.com/waldronlab/TENxIO
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Hi @LiNk-NY
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: TENxIO
Type: Package
Title: Import methods for 10X Genomics files
Version: 0.99.3
Authors@R:
person(
"Marcel", "Ramos", , "[email protected]",
c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")
)
Depends: R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
Imports:
BiocBaseUtils,
BiocGenerics,
BiocIO,
GenomeInfoDb,
GenomicRanges,
Matrix,
MatrixGenerics,
methods,
RCurl,
readr,
R.utils,
S4Vectors,
utils
Suggests:
BiocStyle,
ExperimentHub,
HDF5Array,
knitr,
RaggedExperiment,
rhdf5,
rmarkdown,
Rsamtools,
tinytest
Description: Provides a structured S4 approach to importing data files from
the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene
Expresssion data among other data types. The main Bioconductor data
representations used are SingleCellExperiment and RaggedExperiment.
biocViews: Software, Infrastructure, DataImport, SingleCell
VignetteBuilder: knitr
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
BugReports: https://github.com/waldronlab/TENxIO/issues
URL: https://github.com/waldronlab/TENxIO
Collate:
'TENxFile-class.R'
'TENxFileList-class.R'
'TENxFragments-class.R'
'TENxH5-class.R'
'TENxIO-package.R'
'TENxMTX-class.R'
'TENxPeaks-class.R'
'utils.R'
I've not looked at the package closely, but has the design and implications of this package been discussed/planned with the DropletUtils and SpatialExperiment authors, which already have DropletUtils::read10xCounts(), DropletUtils::read10xMolInfo(), and SpatialExperiment::read10xVisium()?
CC: @ltla, @drighelli
For DropletUtils: I have wanted to split the 10X-specific methods into a separate package, so as to avoid having to deal with the minutiae of keeping up with Cellranger. If this package can provide drop-in replacements for the various 10X processing functions (read10xCounts being the most obvious candidate, but also the various molecule info-reading files as well), then I would not be opposed to deprecating those functions in DropletUtils and pointing to this package. (cc @jonathangriffiths)
For SpatialExperiment: my 2c would be that it would be nice to distinguish between the SpatialExperiment data structure, which is intended to be technology-agnostic; and the Visium-specific methods for reading in such a structure, which could conceivably live in another package. The benefit would be that we achieve a clearly defined interface between the data structure and a specific technology; the downside is that it becomes harder for them to co-evolve.
Hi @PeteHaitch and @LTLA !
Dario @drighelli had pointed me to the functionality in https://github.com/drighelli/read10xMultiome which should be covered by this package. I can also work with Dario to support 10X Visium data or have this supported in another package.
I haven't discussed with Aaron @LTLA but I'd be happy to and provide drop-in replacement functionality.
I also agree with Aaron RE: SpatialExperiment in that the infrastructure and data specifications should be kept separate.
Best, Marcel
Thanks for directing me to this conversation, I also think that could be good to have common IO functionalities for 10x outputs in a common package.
Btw, the main author of the read10xVisium function is @HelenaLC, so I think it's good to involve her in this discussion.
Dario
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
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Received a valid push on git.bioconductor.org; starting a build for commit id: 612468475164925eb4fa0fc834af3661f8ccf74e
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/TENxIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @LiNk-NY,
Thank you for submitting TENxIO to Bioconductor. The package is already in reasonably good shape.
However, I do think TENxIO requires comparison to existing Bioconductor solutions for importing 10x Genomics files into R, namely DropletUtils and some of the functionality in SpatialExperiment. The package name sort of suggests that TENxIO is the solution for importing 10x files, but in my testing it was limited to certain types of 10x files and it wasn't clear to me which ones are supported. It would be preferable to have a canonical/preferred Bioconductor package and methods to address this topic rather than multiple packages with overlapping and slightly different approaches.
For acceptance into Bioconductor, there are a number of Required points, as well as Recommended points, that I would ask you to first please address. Would you please provide line-by-line comments to my initial review so that I know what changes I'm looking for in my re-review.
Cheers, Pete
Required
- [ ] Please be more precise about which 10x H5 files are supported. I tried a few examples and encountered problems. For example:
suppressPackageStartupMessages(library(DropletUtils))
suppressPackageStartupMessages(library(DropletTestFiles))
suppressPackageStartupMessages(library(TENxIO))
path <- getTestFile(
"tenx-3.1.0-5k_pbmc_protein_v3/1.0.0/filtered.h5",
prefix = TRUE)
#> snapshotDate(): 2022-10-03
#> see ?DropletTestFiles and browseVignettes('DropletTestFiles') for documentation
#> loading from cache
sce1 <- read10xCounts(path, type = "HDF5")
sce2 <- import(TENxH5(path))
#> Warning: File extension is not 'h5'; import may fail
#> Error in rhdf5::h5read(path(x), paste0(group, x@ranges), list(rows), s3 = remote): Object 'matrix/features/interval' does not exist in this HDF5 file.
Created on 2022-10-04 with reprex v2.0.2
Session info
sessioninfo::session_info()
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#>
#> ──────────────────────────────────────────────────────────────────────────────
- [ ] Related to the above, the lack of support for importing version 2 TENxH5 files (which are used in the vignette) seems like it should be addressed prior to an initial release; is it realistic to add support for these prior to the next release?
suppressPackageStartupMessages(library(TENxIO))
hub <- ExperimentHub::ExperimentHub()
#> snapshotDate(): 2022-10-03
fname <- hub[["EH1039"]]
#> see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
#> loading from cache
con <- TENxFile(fname, extension = "h5", group = "mm10", version = "2")
#> Warning: 'group' not in known 10X groups: matrix, outs
import(con)
#> Error in import(con): Version 2 not supported yet.
Created on 2022-10-04 with reprex v2.0.2
Session info
sessioninfo::session_info()
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#> setting value
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#> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0)
#> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0)
#> RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.2.1)
#> readr 2.1.3 2022-10-01 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
#> rhdf5 * 2.41.1 2022-06-21 [1] Bioconductor
#> rhdf5filters 1.9.0 2022-04-26 [1] Bioconductor
#> Rhdf5lib 1.19.2 2022-05-13 [1] Bioconductor
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.0)
#> RSQLite 2.2.17 2022-09-10 [1] CRAN (R 4.2.0)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
#> S4Vectors * 0.35.4 2022-09-18 [1] Bioconductor
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> shiny 1.7.2 2022-07-19 [1] CRAN (R 4.2.0)
#> SingleCellExperiment * 1.19.1 2022-09-30 [1] Bioconductor
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.0)
#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0)
#> SummarizedExperiment * 1.27.3 2022-09-15 [1] Bioconductor
#> TENxBrainData * 1.17.0 2022-04-27 [1] Bioconductor
#> TENxIO * 0.99.4 2022-10-03 [1] Bioconductor
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
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#> vctrs 0.4.2 2022-09-29 [1] CRAN (R 4.2.1)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.33 2022-09-12 [1] CRAN (R 4.2.0)
#> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.0)
#> XVector 0.37.1 2022-08-25 [1] Bioconductor
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
#> zlibbioc 1.43.0 2022-04-26 [1] Bioconductor
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
- [ ] What about other 10x file types, such as those from Visium (where currently a user would typically import using
SpatialExperiment::read10xVisium())? Is it intended that TENxIO is used for these files? - [ ] In light of the above, I think the package name might need some adjustment to better reflect the package's scope (i.e. what types of 10x Genomics files the package supports). This package documentation and vignette also needs to review/compare this package to other packages with similar functionality or scope (e.g., DropletUtils,
SpatialExperiment::read10xVisium(), there may be others). - [ ]
R CMD checkerrors for me (macOS Intel). The specific error is a lack of support for S3 VFD in Rhdf5lib (see below). This may be specific to my system but have you checked TENxIO on this platform? In any case, I think this should be handled gracefully by the underlying function (and its tests).
suppressPackageStartupMessages(library(TENxIO))
pbmc_url <-
"https://raw.githubusercontent.com/waldronlab/TENxIO/devel/inst/extdata/10k_pbmc_ATACv2_f_bc_ex.h5"
remoteh5 <- TENxFile(pbmc_url)
#> Error in H5Pset_fapl_ros3(fapl, s3credentials): Rhdf5lib was not compiled with support for the S3 VFD
Rhdf5lib::pkgconfig()
#> "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib/libhdf5.a" -L"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/lib" -lsz -laec -lz -ldl -lm
Created on 2022-10-04 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23)
#> os macOS Big Sur ... 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_AU.UTF-8
#> ctype en_AU.UTF-8
#> tz Australia/Melbourne
#> date 2022-10-04
#> pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
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#> BiocBaseUtils 0.99.12 2022-09-02 [1] Bioconductor
#> BiocGenerics * 0.43.4 2022-09-11 [1] Bioconductor
#> BiocIO 1.7.1 2022-05-06 [1] Bioconductor
#> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
#> DelayedArray 0.23.2 2022-09-15 [1] Bioconductor
#> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
#> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.0)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
#> GenomeInfoDb * 1.33.7 2022-09-07 [1] Bioconductor
#> GenomeInfoDbData 1.2.9 2022-09-30 [1] Bioconductor
#> GenomicRanges * 1.49.1 2022-08-18 [1] Bioconductor
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0)
#> hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.0)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0)
#> IRanges * 2.31.2 2022-08-18 [1] Bioconductor
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.0)
#> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1)
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#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
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#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
#> RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.2.1)
#> readr 2.1.3 2022-10-01 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
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#> rhdf5filters 1.9.0 2022-04-26 [1] Bioconductor
#> Rhdf5lib 1.19.2 2022-05-13 [1] Bioconductor
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.0)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
#> S4Vectors * 0.35.4 2022-09-18 [1] Bioconductor
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> SingleCellExperiment * 1.19.1 2022-09-30 [1] Bioconductor
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.0)
#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0)
#> SummarizedExperiment * 1.27.3 2022-09-15 [1] Bioconductor
#> TENxIO * 0.99.4 2022-10-03 [1] Bioconductor
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
#> tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
#> vctrs 0.4.2 2022-09-29 [1] CRAN (R 4.2.1)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.33 2022-09-12 [1] CRAN (R 4.2.0)
#> XVector 0.37.1 2022-08-25 [1] Bioconductor
#> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
#> zlibbioc 1.43.0 2022-04-26 [1] Bioconductor
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
- [ ] Please use a smaller
.h5file in the vignette and documentation (rather thanEH1039). I think it's a bit unreasonable to require a 3.9 GB download to run the example onTENxFileman page (and also used in the vignette). - [ ] Please clarify the return value of the
import,TENxMTX-method; it currently returns a SummarizedExperiment, but the?TENxMTXand?TENxIOdocumentation seems to imply it will return a bare dgCMatrix. - [ ]
import()on a TENxMTX produces notesas(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead; please address this by following the recommended fix of the Matrix authors. - [ ]
import,TENxFileList-methodwill likely fail for older 10x tarballs (version 2) because the file names in 10x tarballs vary with version (e.g.,features.tsv.gz(v3) vs.genes.tsv.gz(v2)). This should be gracefully handled or support added for older versions.. - [ ]
BiocCheck::BiocCheck()recommendsAvoid system() ; use system2(). - [ ] Please add an 'Introduction' section to the vignette.
Recommended
- [ ] Strongly recommend testing TENxIO functionality using some of the example files included in DropletTestFiles (perhaps adding additional example files as necessary, e.g., from the 10x multiome or ATAC-seq kits). For example, see how these are implemeted as 'long tests' in DropletUtils.
- [ ] What does this warning mean and should it be occurring?
suppressPackageStartupMessages(library(TENxIO))
hub <- ExperimentHub::ExperimentHub()
#> snapshotDate(): 2022-10-03
fname <- hub[["EH1039"]]
#> see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
#> loading from cache
TENxFile(fname, extension = "h5", group = "mm10", version = "2")
#> Warning: 'group' not in known 10X groups: matrix, outs
#> TENxH5 object
#> resource: /Users/Peter/Library/Caches/org.R-project.R/R/ExperimentHub/48e4b14df09_1039
#> projection: SingleCellExperiment
#> dim: 27998 1306127
#> rownames: ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742
#> rowData names(3): ID Symbol Type
#> Type: ENSMUSG00000025900 ENSMUSG00000025902 ... ENSMUSG00000102343 ENSMUSG00000109048
#> colnames: AAACCTGAGATAGGAG-1 AAACCTGAGCGGCTTC-1 ... TTTGTCAGTTAAAGTG-133 TTTGTCATCTGAAAGA-133
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23)
#> os macOS Big Sur ... 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_AU.UTF-8
#> ctype en_AU.UTF-8
#> tz Australia/Melbourne
#> date 2022-10-04
#> pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
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#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
#> rhdf5 * 2.41.1 2022-06-21 [1] Bioconductor
#> rhdf5filters 1.9.0 2022-04-26 [1] Bioconductor
#> Rhdf5lib 1.19.2 2022-05-13 [1] Bioconductor
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
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#> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0)
#> SummarizedExperiment * 1.27.3 2022-09-15 [1] Bioconductor
#> TENxBrainData * 1.17.0 2022-04-27 [1] Bioconductor
#> TENxIO * 0.99.4 2022-10-03 [1] Bioconductor
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
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#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
#> vctrs 0.4.2 2022-09-29 [1] CRAN (R 4.2.1)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.33 2022-09-12 [1] CRAN (R 4.2.0)
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#> XVector 0.37.1 2022-08-25 [1] Bioconductor
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#> zlibbioc 1.43.0 2022-04-26 [1] Bioconductor
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
- [ ] In the vignette there's a note, "Future versions of the package could support alternative representations to SingleCellExperiment"; what does this mean?
- [ ] Recommend running
spelling::spell_check_package(). - [ ] Initially, I didn't have the RaggedExperiment package installed, and so when trying
import(tfr)(from the vignette) I received the error:Error: Install 'RaggedExperiment' to use 'import'; you might consider providing instructions for installing this package usingBiocManager::install()(I'm not sure if Bioconductor has a standardised approach to notify users of such installation issues?) - [ ] Why
roiinstead ofwhichforTENxFragments()? My understanding is that this argument gets passed to thewhichargument of the ScanBamParam object, so it might make sense to use the same argument name. - [ ]
help("TENxH5-class", "TENxIO")refers toxas a SummarizedExperiment object but it's a TENxH5 object isn't it? - [ ] In
DESCRIPTION,Collateshould beCollates.
Hi Pete, @PeteHaitch
Thank you for the comprehensive review. Please see my responses below.
Best, Marcel
Required
- [x] Please be more precise about which 10x H5 files are supported. I tried a few examples and encountered problems. For example:
I've added support for files without 'interval' information. You can now read this in with:
- [x] Related to the above, the lack of support for importing version 2 TENxH5 files (which are used in the vignette) seems like it should be addressed prior to an initial release; is it realistic to add support for these prior to the next release?
Support for version 2 is added. It will import a plain SingleCellExperiment.
Session info
- [x] What about other 10x file types, such as those from Visium (where currently a user would typically import using
SpatialExperiment::read10xVisium())? Is it intended that TENxIO is used for these files?
I will let Dario @drighelli or Helena @HelenaLC comment here. They are welcomed to contribute to the package. I would rather not duplicate code already in SpatialExperiment and it is a good idea to separate the I/O operations specific to the technology from the data structure implementation.
- [x] In light of the above, I think the package name might need some adjustment to better reflect the package's scope (i.e. what types of 10x Genomics files the package supports). This package documentation and vignette also needs to review/compare this package to other packages with similar functionality or scope (e.g., DropletUtils,
SpatialExperiment::read10xVisium(), there may be others).
I have added a note in the Introduction detailing the scope of the package.
- [x]
R CMD checkerrors for me (macOS Intel). The specific error is a lack of support for S3 VFD in Rhdf5lib (see below). This may be specific to my system but have you checked TENxIO on this platform? In any case, I think this should be handled gracefully by the underlying function (and its tests).
I do not have access to a Mac. I think the BBS is configured properly with this support. Once accepted, I will take a look at the build report. Thanks for bringing this up.
- [x] Please use a smaller
.h5file in the vignette and documentation (rather thanEH1039). I think it's a bit unreasonable to require a 3.9 GB download to run the example onTENxFileman page (and also used in the vignette).
The builders should have it in memory but I have made this chunk eval=FALSE
and added a note for anyone running this that it is a big file.
- [x] Please clarify the return value of the
import,TENxMTX-method; it currently returns a SummarizedExperiment, but the?TENxMTXand?TENxIOdocumentation seems to imply it will return a bare dgCMatrix.- [x]
import()on a TENxMTX produces notesas(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead; please address this by following the recommended fix of the Matrix authors.- [x]
import,TENxFileList-methodwill likely fail for older 10x tarballs (version 2) because the file names in 10x tarballs vary with version (e.g.,features.tsv.gz(v3) vs.genes.tsv.gz(v2)). This should be gracefully handled or support added for older versions..- [x]
BiocCheck::BiocCheck()recommendsAvoid system() ; use system2().
It looks like it's finding these calls in the inst/scripts directory. That
check should be restricted to only files in the R folder.
- [x] Please add an 'Introduction' section to the vignette.
Recommended
- [x] Strongly recommend testing TENxIO functionality using some of the example files included in DropletTestFiles (perhaps adding additional example files as necessary, e.g., from the 10x multiome or ATAC-seq kits). For example, see how these are implemeted as 'long tests' in DropletUtils.
- [x] What does this warning mean and should it be occurring?
This warning is for files that don't have a file extension, namely those in
ExperimentHub. It is just a warning so that the user is aware that they
are attempting to import files that may potentially fail.
- [x] In the vignette there's a note, "Future versions of the package could support alternative representations to SingleCellExperiment"; what does this mean?
- [x] Recommend running
spelling::spell_check_package().- [x] Initially, I didn't have the RaggedExperiment package installed, and so when trying
import(tfr)(from the vignette) I received the error:Error: Install 'RaggedExperiment' to use 'import'; you might consider providing instructions for installing this package usingBiocManager::install()(I'm not sure if Bioconductor has a standardised approach to notify users of such installation issues?)
There is no standardized approach but using BiocManager is understood.
I've added a BiocManager style error message for convenience.
- [x] Why
roiinstead ofwhichforTENxFragments()? My understanding is that this argument gets passed to thewhichargument of the ScanBamParam object, so it might make sense to use the same argument name.- [x]
help("TENxH5-class", "TENxIO")refers toxas a SummarizedExperiment object but it's a TENxH5 object isn't it?- [x] In
DESCRIPTION,Collateshould beCollates.
AFAIK, Collate is the field described in Writing R
Extensions and
auto-generated by roxygen2
Received a valid push on git.bioconductor.org; starting a build for commit id: 055930139afa02c9e4d72caa52d1b858ada7cdb6
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/TENxIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi all, following up here regarding some of the discussion above. Is the plan to essentially move DropletUtils::read10xCounts() and SpatialExperiment::read10xVisium() into this package instead?
I think this could make sense, since it would make a clearer distinction between the underlying data structure and loader / helper functions.
This could also be a good opportunity to resolve some outstanding inconsistencies we currently have in SpatialExperiment between default column names in SCE and SPE objects, mentioned in https://github.com/drighelli/SpatialExperiment/issues/100
Tagging @drighelli @HelenaLC @drisso @stephaniehicks FYI
Hi @LiNk-NY,
Thank you for making the above changes. There are still a few issues that I think require further changes or that I noticed following your recent changes.
Regarding the integration/subsuming of functionality of DropletUtils/SpatialExperiment: with the release deadline so soon I think this will have to be done over subsequent release cycles and in a progressive and backwards-compatible way.
Thanks, Pete
Required
- [ ] The 'Introduction' of the vignette is still too vague about which 10X files are supported. Please think of a new user wanting to know whether this package or another BioC package is suitable for their files. Something like a table that summarises the 10x assays (3' and 5' scRNA-seq, scATAC-seq, multiome, Visium, etc.) and file types and which packages support which assays and file types. The table in 'Supported Formats' is close, but lacks assay details and comparisons to existing solutions.
- [ ] Some behaviour of
TENxH5()andimport,TENxH5,ANY,ANY-methodrequires better documentation:- [ ] The
ranges = NA_charactertrick for reading in a 10X H5 file without 'interval' information is mentioned in the vignette but not in the man pages. - [ ]
import,TENxH5,ANY,ANY-methodappliesSingleCellExperiment::splitAltExperiment()but this is undocumented. - [ ] Do
import()methods in the package also applySingleCellExperiment::splitAltExperiment()? If so, please document.
- [ ] The
suppressPackageStartupMessages(library(DropletUtils))
suppressPackageStartupMessages(library(DropletTestFiles))
suppressPackageStartupMessages(library(TENxIO))
path <- getTestFile(
"tenx-3.1.0-5k_pbmc_protein_v3/1.0.0/filtered.h5",
prefix = TRUE)
#> snapshotDate(): 2022-10-03
#> see ?DropletTestFiles and browseVignettes('DropletTestFiles') for documentation
#> loading from cache
# import() itnernally applies SingleCellExperiment::splitAltExperiment().
sce <- import(TENxH5(path, ranges = NA_character_))
#> Warning: File extension is not 'h5'; import may fail
sce
#> class: SingleCellExperiment
#> dim: 33538 5247
#> metadata(0):
#> assays(1): counts
#> rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
#> ENSG00000268674
#> rowData names(0):
#> colnames(5247): AAACCCAAGAGACAAG-1 AAACCCAAGGCCTAGA-1 ...
#> TTTGTTGCATTGCCGG-1 TTTGTTGGTCCGGCAT-1
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: Gene Expression
#> altExpNames(1): Antibody Capture
Created on 2022-10-11 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
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#> ctype en_AU.UTF-8
#> tz Australia/Melbourne
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#>
#> ──────────────────────────────────────────────────────────────────────────────
- [ ] The
?TENxIOdocumentation (and the table in the vignette and README) still implies that theimport,TENxMTX-methodwill return a bare dgCMatrix. - [ ] Please add your note of explanation to the vignette about why this gives a warning (along the lines of what you replied to me, 'This warning is for files that don't have a file extension, namely those in ExperimentHub. It is just a warning so that the user is aware that they are attempting to import files that may potentially fail.' ....) .
suppressPackageStartupMessages(library(TENxIO))
hub <- ExperimentHub::ExperimentHub()
#> snapshotDate(): 2022-10-03
fname <- hub[["EH1039"]]
#> see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
#> loading from cache
TENxFile(fname, extension = "h5", group = "mm10", version = "2")
#> Warning: 'group' not in known 10X groups: matrix, outs
#> TENxH5 object
#> resource: /Users/Peter/Library/Caches/org.R-project.R/R/ExperimentHub/48e4b14df09_1039
#> projection: SingleCellExperiment
#> dim: 27998 1306127
#> rownames: ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742
#> rowData names(3): ID Symbol Type
#> Type: ENSMUSG00000025900 ENSMUSG00000025902 ... ENSMUSG00000102343 ENSMUSG00000109048
#> colnames: AAACCTGAGATAGGAG-1 AAACCTGAGCGGCTTC-1 ... TTTGTCAGTTAAAGTG-133 TTTGTCATCTGAAAGA-133
Created on 2022-10-11 with reprex v2.0.2
Session info
sessioninfo::session_info()
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Recommended
- [ ] Strongly recommend testing TENxIO functionality using some of the example files included in DropletTestFiles (perhaps adding additional example files as necessary, e.g., from the 10x multiome or ATAC-seq kits). For example, see how these are implemeted as 'long tests' in DropletUtils. Correct data import is a critical step of any workflow, so it needs to be widely tested. AFAICT DropletTestFiles provides a great set of example files for adding such tests in TENxIO (e.g., it's how I identified limitations of prior versions of TENxIO).
Required
- [x] The 'Introduction' of the vignette is still too vague about which 10X files are supported. Please think of a new user wanting to know whether this package or another BioC package is suitable for their files. Something like a table that summarises the 10x assays (3' and 5' scRNA-seq, scATAC-seq, multiome, Visium, etc.) and file types and which packages support which assays and file types. The table in 'Supported Formats' is close, but lacks assay details and comparisons to existing solutions.
I've added more information about the experiments that are covered based on the listings in the 10X website.
- [x] Some behaviour of
TENxH5()andimport,TENxH5,ANY,ANY-methodrequires better documentation
- [x] The
ranges = NA_charactertrick for reading in a 10X H5 file without 'interval' information is mentioned in the vignette but not in the man pages.- [x]
import,TENxH5,ANY,ANY-methodappliesSingleCellExperiment::splitAltExperiment()but this is undocumented.- [x] Do
import()methods in the package also applySingleCellExperiment::splitAltExperiment()? If so, please document.- [x] The
?TENxIOdocumentation (and the table in the vignette and README) still implies that theimport,TENxMTX-methodwill return a bare dgCMatrix.- [x] Please add your note of explanation to the vignette about why this gives a warning (along the lines of what you replied to me, 'This warning is for files that don't have a file extension, namely those in ExperimentHub. It is just a warning so that the user is aware that they are attempting to import files that may potentially fail.' ....) .
Recommended
- [x] Strongly recommend testing TENxIO functionality using some of the example files included in DropletTestFiles (perhaps adding additional example files as necessary, e.g., from the 10x multiome or ATAC-seq kits). For example, see how these are implemeted as 'long tests' in DropletUtils. Correct data import is a critical step of any workflow, so it needs to be widely tested. AFAICT DropletTestFiles provides a great set of example files for adding such tests in TENxIO (e.g., it's how I identified limitations of prior versions of TENxIO).
Hi Pete,
Thank for the feedback. I've implemented some long tests. I will continue to add more unit tests with additional files in the DropletTestFiles package. For now, I've added a few. These help improve the codebase of the package. Thank you!
Best regards, Marcel
Received a valid push on git.bioconductor.org; starting a build for commit id: 12ed99b7cb23395853fc3f0097f74890a32f2f4f
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/TENxIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: a4d61b6f85067b9328ab984a5c86151c9b94755b
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/TENxIO to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thank you for addressing the requested changes and engaging with the review process, @LiNk-NY. I'm happy to accept TENxIO into Bioconductor!
A couple of final things:
- [ ] Please keep an eye on the builds to see if the lack of support for S3 VFD in Rhdf5lib is a general issue affecting macOS (initially flagged in https://github.com/Bioconductor/Contributions/issues/2753#issuecomment-1266309537)
- [ ] The
?TENxIOdocumentation still implies that theimport,TENxMTX-methodwill return a bare dgCMatrix.
Thank you for your contribution.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at
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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("TENxIO"). The package 'landing page' will be created at
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If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.
Thanks Pete! @PeteHaitch
- [ ] Please keep an eye on the builds to see if the lack of support for S3 VFD in Rhdf5lib is a general issue affecting macOS (initially flagged in TENxIO #2753 (comment))
I will keep an eye out.
- [x] The
?TENxIOdocumentation still implies that theimport,TENxMTX-methodwill return a bare dgCMatrix.
Ah, I see the file now. It was in TENxIO-package.R. Thanks again!