QTLExperiment

[dunstone-a]

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[bioc-issue-bot]

Hi @dunstone-a

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: QTLExperiment
Type: Package
Date: 2022-11-08
Title: S4 classes for QTL summary statistics and metadata
Version: 0.99.0
Authors@R: c(
    person("Christina", "Del Azodi", role=c("aut"), email="cazodi@svi.edu.au"), 
    person("Davis","McCarthy", role=c("ctb"), email="dmccarthy@svi.edu.au"),
    person("Amelia","Dunstone", role=c("cre", "ctb"), email="amelia.dunstone@svi.edu.au", comment=c(ORCID="0009-0009-6426-1529")))
License: GPL-3
Encoding: UTF-8
Depends: 
    SummarizedExperiment
Imports: 
    methods,
    rlang,
    checkmate,
    dplyr,
    collapse,
    vroom,
    tidyr,
    tibble,
    utils,
    stats,
    ashr,
    S4Vectors,
    BiocGenerics
Suggests: 
    testthat,
    BiocStyle, 
    knitr, 
    rmarkdown,
    covr
Description: QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states.
    It is based on the 'SummarizedExperiment' class and contains functions for creating, merging, and subsetting objects.
    'QTLExperiment' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.
biocViews: FunctionalGenomics, DataImport, DataRepresentation, Infrastructure, Sequencing, SNP, Software
VignetteBuilder: knitr
RoxygenNote: 7.2.3

[lshep]

In your vignette you are pulling example data directly from github ebi <- read.csv("https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/data_tables/dataset_metadata.tsv", sep = "\t") . This smaller subset of data should be included in the package as we do not allow download of external data from github.

[dunstone-a]

Hi @lshep , thanks for this. I have now updated the package so that the relevant data is included in the folder inst/extdata. There is a script in inst/script that downloads the data from the EBI database and saves 4 data files which are used in the vignette, tests, and examples.

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): QTLExperiment_0.99.2.tar.gz macOS 12.6.5 Monterey: QTLExperiment_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/QTLExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: eb66ecd3f81dec90de4becb24a77252a21832409

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "WARNINGS". 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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): QTLExperiment_0.99.3.tar.gz macOS 12.6.5 Monterey: QTLExperiment_0.99.3.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/QTLExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

Quick round of initial comments to get the ball rolling... please comment back with what has/has not been addressed, or anything you would like to discuss/more details on; thanks!

majorish

• [ ] admittedly not 100% sure about what is fixed/flexible in a given QTLExperiment object for standard analyses, but I notice that the following operations pass without issues, and make rowData, int_rowData, and rownames appear out of synch (though the latter is anyways optional, I guess). Would this cause downstream operations to break? Would it be worth considering to revise any replacement method(s)? I think my confusion comes from the fact that I am reading the word "protected" here and there, but don't see this being implemented

# run `QTLExperiment` example to obtain
qtle <- ...

# both of these work/don't affect anything else
# so that things appear out of synch afterwards
rowData(qtle)$feature_id <- sample(rowData(qtle)$feature_id)
int_rowData(qtle)$.feature_id <- sample(int_rowData(qtle)$.feature_id)

# similarly, this works
rowData(qtle) <- NULL
int_rowData(qtle) <- DataFrame()

minor

• [ ] in the README, please update Bioc installation instructions (i.e., how to install the package - not its dependencies - using BiocManager::install())

• [ ] in the vignette, please also update installation instructions to use BiocManager::install()

• [ ] in the vignette, considering using BiocStyle functions to directly hyperlink external packages, e.g., r BiocStyle::Biocpkg("SummarizedExperiment") (there are analogous functions for packages hosten through CRAN, GitHub etc.)

• [ ] unit test coverage is ok, but might be worth improving (devtools::test_coverage() gives me 60%, mostly due to missing tests for qtle_internals.R)

• [ ] in the NEWS, remember to keep track of changes, in non-technical language, in the code from one version to the next

• [ ] in the DESCRIPTION, consider adding URL: and BugReports: fields pointing to https://github.com/dunstone-a/QTLExperiment and .../issues, respectively

• [ ] BiocCheck() WARNING: missing value sections (roxygen tag #' @return) for assays.Rd, internals.Rd and miscellaneous.Rd

• [ ] I understand coding styles are a personal thing, but we (inspired by Hadley Wickham, I think) recommend 4-space tab indentation vs. vertical alignment, and spaces around assignment and logical operators, but not equality signs as used for arguments; this makes the code a lot easier to read by producing less unnecessary white space (see here for details) ...especially in the vignette, which is typically displayed online in HTML format, adhering to this style consistently makes things a little easier to grasp

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 0d7079ba0d86982ef884234a1ef688e67559a538

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "WARNINGS". 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.

The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: QTLExperiment_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): QTLExperiment_0.99.4.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/QTLExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 773ac0c3ff2f8c485a922611ebf9780cd3f23865

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "WARNINGS". 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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): QTLExperiment_0.99.5.tar.gz macOS 12.6.5 Monterey: QTLExperiment_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/QTLExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[dunstone-a]

Thank you for your comments @HelenaLC ! Really appreciate you looking into this.

admittedly not 100% sure about what is fixed/flexible in a given QTLExperiment object for standard analyses, but I notice that the following operations pass without issues, and make rowData, int_rowData, and rownames appear out of synch (though the latter is anyways optional, I guess). Would this cause downstream operations to break? Would it be worth considering to revise any replacement method(s)? I think my confusion comes from the fact that I am reading the word "protected" here and there, but don't see this being implemented

It is intended that feature_id, state_id and variant_id are modified through the specal setters feature_id(), state_id() and variant_id(). As you point out, if these fields are altered manually then it can lead to inconsistencies between the rownames and the rowData(), which is definitely not ideal. This is talked about a little in the section "Manually syncing metadata" in the vignette. The function recover_qtle_ids can be used if rowData becomes out of sync, by replacing colData and rowData with the internal versions of these (which should not be altered by the end user).

It would be nice if the following were equivalent:

rowData(qtle)$feature_id <- sample(rowData(qtle)$feature_id)
feature_id(qtle) <- sample(rowData(qtle)$feature_id)

But as it is currently, feature_id will only be properly changed using the dedicated setter. I will look to implement this in the future as it does affect functions in the additional package multistateQTL (to be submitted next round of Bioconductor).

in the README, please update Bioc installation instructions (i.e., how to install the package - not its dependencies - using BiocManager::install()) in the vignette, please also update installation instructions to use BiocManager::install()

The installation instructions for both have been updated to use Bioconductor.

in the vignette, considering using BiocStyle functions to directly hyperlink external packages, e.g., r BiocStyle::Biocpkg("SummarizedExperiment") (there are analogous functions for packages hosted through CRAN, GitHub etc.)

I have hyperlinked to SummarizedExperiment and vroom using Biocpkg and CRANpkg.

unit test coverage is ok, but might be worth improving (devtools::test_coverage() gives me 60%, mostly due to missing tests for qtle_internals.R)

I've added some tests for the internal functions but will also add more tomorrow.

in the NEWS, remember to keep track of changes, in non-technical language, in the code from one version to the next

I have started the NEWS file and will add to this with changes relevant to the operation of the package.

in the DESCRIPTION, consider adding URL: and BugReports: fields pointing to https://github.com/dunstone-a/QTLExperiment and .../issues, respectively

Added to the description.

BiocCheck() WARNING: missing value sections (roxygen tag #' @return) for assays.Rd, internals.Rd and miscellaneous.Rd

I have split up the "Miscellaneous" documentation file into two files, one for the object version information and one for the name of the object. Hopefully this will be a bit clearer.

I have added a return section for the remaining documentation pages now, in version 0.99.6.

I understand coding styles are a personal thing, but we (inspired by Hadley Wickham, I think) recommend 4-space tab indentation vs. vertical alignment, and spaces around assignment and logical operators, but not equality signs as used for arguments; this makes the code a lot easier to read by producing less unnecessary white space (see here for details)

I have removed spaces around the equality signs in arguments. As for vertical alignment vs 4 spaces, should I switch to B or C below?

# A: what I was doing
input <- data.frame(state=state, 
                    path=paste0(input_path, "/GTEx_tx_", state, ".tsv"))
# B: 
input <- data.frame(state=state, 
    path=paste0(input_path, "/GTEx_tx_", state, ".tsv"))
# C: 
input <- data.frame(
    state=state, 
    path=paste0(input_path, "/GTEx_tx_", state, ".tsv"))

Also not sure what is best for cases with two or more levels, e.g.

new_colData <- DataFrame(list(some_info1=LETTERS[1:ncol(qtle4)],
                              some_info2=c(1:ncol(qtle4))))

Thanks, Amelia

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f0b351a2ebaf116ad35c4c9160716f4b0fe83b6d

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): QTLExperiment_0.99.6.tar.gz macOS 12.6.5 Monterey: QTLExperiment_0.99.6.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/QTLExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

Thanks for addressing earlier comments - all looks in order to me now (regarding strikt Bioc requirements); just leaving these comments for your information/something to consider in the future perhaps (especially the last one!):

• Re indentation/spacing: either B or C are fine, depending on personal preference, and the length of the 1st argument perhaps - in any case, I'd say these are preferable over vertical indentation in any case (just imagine a very long variable name and a very long function name, and ending up at 30 characters before starting the (...)
• Re NEWS: Hm, the package is at 0.99.6, while the NEWS lists only 0.99.0. Ideally, you'd want every version to appear here, irrespective of whether or not changes are "relevant" (for example, I frequently just put "fixed typo" because some tests/vignette section was broken or similar)... even lack of many changes helps understand when there are significant changes in a given version
• Re rowData<-: Yeah, I agree that this should definitely be addressed in the future. You mentioned that "ideally this should be the same", and it can be! The idea behind implementing an S4 class that inherits from another is that you can control specific requirements for your class, e.g., implementing a custom rowData<- replacement method. See for example SpatialExperiment where this is done to assure sample_ids adhere to certain requirements. I encourage trying to come up with a more robust solution here then "let the user figure it out or, well, bad luck and things just go out of things" ;)

[bioc-issue-bot]

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[lshep]

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