smartid

[Gene233]

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• Repository: https://github.com/DavisLaboratory/smartid

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[bioc-issue-bot]

Hi @Gene233

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: smartid
Title: Scoring and Marker Selection Method Based on Modified TF-IDF
Version: 0.99.1
Authors@R: 
    person("Jinjin", "Chen", email = "chen.j@wehi.edu.au", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0001-7923-5723"))
Description: This package enables automated selection of group specific signature,
    especially for rare population. The package is developed for generating
    specifc lists of signature genes based on TF-IDF modified methods. It can
    also be used as a new gene-set scoring method or data transformation method.
    Multiple visualization functions are implemented in this package.
biocViews: Software, GeneExpression, Transcriptomics
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Collate: 
    'tf_idf_iae_wrappers.R'
    'score.R'
    'AllGenerics.R'
    'gs_score-methods.R'
    'objects.R'
    'plot.R'
    'scale_mgm.R'
    'score-methods.R'
    'select_markers.R'
    'smartid-package.R'
    'top_markers.R'
    'top_markers-methods.R'
Depends: 
    R (>= 4.3)
Imports: 
    dplyr,
    ggplot2,
    graphics,
    Matrix,
    mclust,
    methods,
    mixtools,
    sparseMatrixStats,
    stats,
    SummarizedExperiment,
    tidyr,
    utils
Suggests: 
    BiocStyle,
    dbscan,
    ggpubr,
    knitr,
    rmarkdown,
    scater,
    splatter,
    testthat (>= 3.0.0),
    tidytext,
    UpSetR
VignetteBuilder: knitr
Config/testthat/edition: 3
LazyData: true

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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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 Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): smartid_0.99.1.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/smartid to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fe762f19636d6ada24f4faf01a45b4815d404203

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): smartid_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/smartid to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Gene233]

The warnings should be OK. There is only one warning in the build report WARNING: R CMD check exceeded 10 min requirement. But what I changed is just to add some tests for some functions. And the tests can be done within 1 min on my own PC.

I also did the same check on my own PC and on github actions, both indicating the duration is less than 10 mins. So I suppose this was caused by some random effects and should be fine for a new buiding.

[HelenaLC]

Yeah, also not sure what happened there - proceeding with review for now. First round of comments below. Please respond back with what has/not been addressed how/why not and, of course, any questions you might have - cheers!

• in general, please address the NOTES in the build report to the best of your abilities; many of the points below are just a reiteration of those, and most of them are only acceptable in exceptional cases.

• also, consider having a look at the code-style guidelines here - e.g., 4-space tab indentation, not vertical alignment; spaces around logical operators and after comma, not argument equals etc. - although we don't enforce these, we appreciate consistency (with your own style at least)

misc

• in the README, please add Bioc installation instructions using BiocManager::install()

• related to that, for release, please drop devtools installation instructions from the vignette

• in the DESCRIPTION, please bump R version dependency to >= 4.4

• in the DESCRIPTION, LazyData: should be set to false or removed

• in the DESCRIPTION, the Description: states "TF-IDF modified methods", however, not everyone browsing packages might be familiar with that acronym (e.g., I had to look it up); please spell that out once

• any classes declared by a package should go under AllClasses.R; i.e., renaming objects.R resolves this

docs

• at the core of the package are TF, IDF and IAE, however, I only see a one-liner in the vignette line 117 explaining these, which is rather confusing and missing from the R documentation... maybe spelling this out a little more/different phrasing could help, e.g., "inverse cell frequency" and "average expression" aren't clear to me at all, although I work with single-cell data - per label/group? across everything?; and, "similar to CPM" - meaning what exactly? There are some commented out math-chunks in various scripts - what's happened to those? - though a verbal explanation would already help a lot (in both the R docs and vignette)!

• related, ?calc_sco, ?tf, ?idf, iae spell out acronyms but don't describe the computation (e.g., under details) and output structure (under return value) etc.

• vignette typos/spelling/grammar

  • line 35: specifc -> specific
  • line 111: expectatiion -> expectation
  • line 145: im-balanced -> imbalanced
  • line 170: this gene's -> this genes
  • line 270: tranform -> transform

• for readability, I'd suggest using math-style at line 119 and 243 (and possibly others I missed), i.e., wrapping the computation with single $s in the text ($$ yields centered, out-of line math as already done correctly; $ is for in-line math mode)

• consider hyperlinking external packages using, e.g., BiocStyle::Biocpkg("splatter") (similar functions are available for packages hosted on CRAN and GitHub)

• very minor, but "smartid" is sometimes in plain text, once bold, and usually in code-style; would be nice to be consistent here

• for clarity, might be worth considering to use function() when something is a function (e.g., markers_mclust()) and variable/argument/slot when it is not (e.g., top_m, GeneMean)

code

• please do not use @ for data retrieval and use the corresponding accessor methods instead, e.g., metadata() not x@metadata -- everywhere (also the vignette) -- and the same goes for assignments, e.g., metadata(x)$a <- b not x@metadata$a <- b

• commented out code should be removed for release (see, e.g., select_markers.R, scale_mgm.R, iae_hdb() etc.)

• when subsetting matrices for downstream computations that expect a matrix still, one should always use x[i, j, drop=FALSE]; else, subsetting single rows/columns will return a vector instead, causing failure (see, e.g., idf_prob() but it's all over the place)

• use vapply() instead of sapply() (e.g., tf_idf_iae_wrapper.R) - see here and also the build report - perhaps worth doing a package-wide search (shift+command+F on my Mac) for any sapplys

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b958720e44be896b1973d826243de7bb47565b2b

[Gene233]

Yeah, also not sure what happened there - proceeding with review for now. First round of comments below. Please respond back with what has/not been addressed how/why not and, of course, any questions you might have - cheers!

• in general, please address the NOTES in the build report to the best of your abilities; many of the points below are just a reiteration of those, and most of them are only acceptable in exceptional cases.
• also, consider having a look at the code-style guidelines here - e.g., 4-space tab indentation, not vertical alignment; spaces around logical operators and after comma, not argument equals etc. - although we don't enforce these, we appreciate consistency (with your own style at least)

misc

• in the README, please add Bioc installation instructions using BiocManager::install()
• related to that, for release, please drop devtools installation instructions from the vignette
• in the DESCRIPTION, please bump R version dependency to >= 4.4
• in the DESCRIPTION, LazyData: should be set to false or removed
• in the DESCRIPTION, the Description: states "TF-IDF modified methods", however, not everyone browsing packages might be familiar with that acronym (e.g., I had to look it up); please spell that out once
• any classes declared by a package should go under AllClasses.R; i.e., renaming objects.R resolves this

docs

• at the core of the package are TF, IDF and IAE, however, I only see a one-liner in the vignette line 117 explaining these, which is rather confusing and missing from the R documentation... maybe spelling this out a little more/different phrasing could help, e.g., "inverse cell frequency" and "average expression" aren't clear to me at all, although I work with single-cell data - per label/group? across everything?; and, "similar to CPM" - meaning what exactly? There are some commented out math-chunks in various scripts - what's happened to those? - though a verbal explanation would already help a lot (in both the R docs and vignette)!
• related, ?calc_sco, ?tf, ?idf, iae spell out acronyms but don't describe the computation (e.g., under details) and output structure (under return value) etc.

• vignette typos/spelling/grammar

  • line 35: specifc -> specific
  • line 111: expectatiion -> expectation
  • line 145: im-balanced -> imbalanced
  • line 170: this gene's -> this genes
  • line 270: tranform -> transform
• for readability, I'd suggest using math-style at line 119 and 243 (and possibly others I missed), i.e., wrapping the computation with single $s in the text ($$ yields centered, out-of line math as already done correctly; $ is for in-line math mode)
• consider hyperlinking external packages using, e.g., BiocStyle::Biocpkg("splatter") (similar functions are available for packages hosted on CRAN and GitHub)
• very minor, but "smartid" is sometimes in plain text, once bold, and usually in code-style; would be nice to be consistent here
• for clarity, might be worth considering to use function() when something is a function (e.g., markers_mclust()) and variable/argument/slot when it is not (e.g., top_m, GeneMean)

code

• please do not use @ for data retrieval and use the corresponding accessor methods instead, e.g., metadata() not x@metadata -- everywhere (also the vignette) -- and the same goes for assignments, e.g., metadata(x)$a <- b not x@metadata$a <- b
• commented out code should be removed for release (see, e.g., select_markers.R, scale_mgm.R, iae_hdb() etc.)
• when subsetting matrices for downstream computations that expect a matrix still, one should always use x[i, j, drop=FALSE]; else, subsetting single rows/columns will return a vector instead, causing failure (see, e.g., idf_prob() but it's all over the place)
• use vapply() instead of sapply() (e.g., tf_idf_iae_wrapper.R) - see here and also the build report - perhaps worth doing a package-wide search (shift+command+F on my Mac) for any sapplys

Hi @HelenaLC , thank you very much for your quick response and detailed advice. I've updated based on your suggestions. Here're the details:

• in general, fixed notes as many as possible.
• [x] set false for 'LazyData' in the 'DESCRIPTION'.
• [x] Update R version dependency from 4.3 to 4.4.
• [x] Replace sapply with vapply.
• [x] Replace print() with show().
• [x] Use function instead of accessors @.
• code-style, used styler to tidy the code-style.

misc

• [x] add Bioc installation instructions in README.
• [x] drop devtools installation instructions from the vignette.
• [x] bump R version.
• [x] set false for LazyData.
• [x] spell TF-IDF out in DESCRIPTION.
• [x] rename objects.R as AllClasses.R.

docs

• [x] add details for TF, IDF and IAE in details of functions and vignette.
• [x] fix the typo/grammer/spelling in the vignette.
• [x] use single $s instead of $$s in the text.
• [x] add hyperlink for external packages.
• [x] keep "smartid" consistent as code-style in vignette.
• [x] use function() for real functions and variable/argument... for non-functions.

code

• [x] replace accessors @ with functions.
• [x] removed some commented codes, the rest remaining commented codes will be updated in the future for some extra functions (e.g. threshold for IDF/IAE offset).
• [x] add drop=FALSE when subsetting matrices.
• [x] use vapply() instead of sapply().

Summary

These are my updates in response to your feedback, and I'm glad to discuss specific details of the changes with you.

Cheers, Jinjin

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): smartid_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/smartid to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

Thanks a lot - build report is very clean now and I appreciate the extended documentation on the three terms!

• [ ] typo in the email address at smartid-package.R line 18.
• [ ] couple instances of @ left (sim_sce_test.R line 25 and test-gs_score.R line 27)
• [ ] please add definition of symbols in the corresponding man pages as well (as you did in the vignette), e.g., ?iae has a formula but doesn't say what $n,i,j,\hat{N}_{ij}$ are
• [ ] vignette lines 116+ are formatted rather weirdly (see screenshot)
  • using $$ ... $$ will display centered, out-of-line math, which I would display more nicely/readable equations here
  • au contraire, $ ... $ should rather be used for brief in-line math (e.g., "where $N_{ij}$ is [...]")
  • perhaps worth rendering the vignette yourself and seeing how things are being rendered outside of RStudio (in the html)

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 8ff99c3c5babfc1739f50798dbbb1155cf3b713c

[Gene233]

Thanks a lot - build report is very clean now and I appreciate the extended documentation on the three terms!

• [x] typo in the email address at smartid-package.R line 18.
• [x] couple instances of @ left (sim_sce_test.R line 25 and test-gs_score.R line 27)
• [x] please add definition of symbols in the corresponding man pages as well (as you did in the vignette), e.g., ?iae has a formula but doesn't say what n,i,j,N^ij are

• [x] vignette lines 116+ are formatted rather weirdly (see screenshot)

  • using $$ ... $$ will display centered, out-of-line math, which I would display more nicely/readable equations here
  • au contraire, $ ... $ should rather be used for brief in-line math (e.g., "where Nij is [...]")
  • perhaps worth rendering the vignette yourself and seeing how things are being rendered outside of RStudio (in the html)

Hi @HelenaLC , thank you for your always quick response. I did update what you mentioned above, i.e. fix email adress in smartid-package.R, replace @ in test files and data scripts, add definition of symbols in details, and update equation formats in the vignette.

Hope this looks better now.

Cheers, Jinjin

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): smartid_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/smartid 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: 67a095bc07677a9c37ff88f0546034e2c004dab8

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): smartid_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/smartid to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

much improved, thanks

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[Gene233]

@HelenaLC Thank you so much for your patience and helpful advice to improve my package!

Cheers, Jinjin

[lshep]

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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to keep your GitHub and Bioconductor repositories in sync.

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("smartid"). 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.