PepSetTest

[JmWangBio]

Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor

• Repository: https://github.com/JmWangBio/PepSetTest

Confirm the following by editing each check box to '[x]'

• I understand that by submitting my package to Bioconductor,
  the package source and all review commentary are visible to the
  general public.

• I have read the Bioconductor Package Submission
  instructions. My package is consistent with the Bioconductor
  Package Guidelines.

• I understand Bioconductor Package Naming Policy and acknowledge
  Bioconductor may retain use of package name.

• I understand that a minimum requirement for package acceptance
  is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS.
  Passing these checks does not result in automatic acceptance. The
  package will then undergo a formal review and recommendations for
  acceptance regarding other Bioconductor standards will be addressed.

• My package addresses statistical or bioinformatic issues related
  to the analysis and comprehension of high throughput genomic data.

• I am committed to the long-term maintenance of my package. This
  includes monitoring the support site for issues that users may
  have, subscribing to the bioc-devel mailing list to stay aware
  of developments in the Bioconductor community, responding promptly
  to requests for updates from the Core team in response to changes in
  R or underlying software.

• I am familiar with the Bioconductor code of conduct and
  agree to abide by it.

I am familiar with the essential aspects of Bioconductor software
management, including:

• The 'devel' branch for new packages and features.
• The stable 'release' branch, made available every six
  months, for bug fixes.
• Bioconductor version control using Git
  (optionally via GitHub).

For questions/help about the submission process, including questions about
the output of the automatic reports generated by the SPB (Single Package
Builder), please use the #package-submission channel of our Community Slack.
Follow the link on the home page of the Bioconductor website to sign up.

[bioc-issue-bot]

Hi @JmWangBio

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: PepSetTest
Title: Peptide Set Test
Version: 0.99.0
Authors@R: 
    person("Junmin", "Wang", , "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "YOUR-ORCID-ID"))
Description: Peptide Set Test (PepSetTest) is a peptide-centric strategy to infer differentially expressed proteins in LC-MS/MS proteomics data. 
    This test detects coordinated changes in the expression of peptides originating from the same protein and compares these changes against the rest of the peptidome. 
    Compared to traditional aggregation-based approaches, the peptide set test demonstrates improved statistical power, yet controlling the Type I error rate correctly in most cases. 
    This test can be valuable for discovering novel biomarkers and prioritizing drug targets, especially when the direct application of 
    statistical analysis to protein data fails to provide substantial insights.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
    dplyr,
    limma,
    lme4,
    magrittr,
    MASS,
    matrixStats,
    reshape2,
    stats,
    tibble
Suggests:
    statmod, knitr, rmarkdown, tidyr
biocViews: DifferentialExpression, Regression, Proteomics, MassSpectrometry
VignetteBuilder: knitr

[lshep]

Please see initial comments:

General

• Is it possible to show interopability with current Bioconductor classes
  for LC-MS/MS proteomics data. http://contributions.bioconductor.org/important-bioconductor-package-development-features.html#commonclass

inst

• What are these scripts used for? I do not see them referenced anywhere in
  the package?

man

• Please have a package level man page so when a naive user does
  '?PepSetTest' they get information on how to get started.

vignette

• We advise renaming the vignette to something more unique like
  PepSetTest.Rmd to avoid naming conflicts pending package load order.

• Could you please expand the intro/abstract to compare/contrast to existing
  Bioconductor methodologies to highlight novel approaches.

• Please show an example using Bioconductor common classes for MS data.

[JmWangBio]

Thanks for the comments! Please see my response below:

Please see initial comments:

General

* [X]  Is it possible to show interopability with current Bioconductor classes
  for LC-MS/MS proteomics data. http://contributions.bioconductor.org/important-bioconductor-package-development-features.html#commonclass

The interopability with SummarizedExperiment, a common class for proteomics data, is now demonstrated in the revised package.

inst

* [ ]  What are these scripts used for? I do not see them referenced anywhere in
  the package?

These scripts can be used to reproduce the analysis shown in Wang et al (2024) Bioinformatics 40(5):btae270, as indicated in the "Code availability" section of the paper. The purpose of these scripts is now clarified in the vignette.

man

* [ ]  Please have a package level man page so when a naive user does
  '?PepSetTest' they get information on how to get started.

A package-level man page has been added.

vignette

* [ ]  We advise renaming the vignette to something more unique like
  PepSetTest.Rmd to avoid naming conflicts pending package load order.

The vignette has been renamed as suggested.

* [ ]  Could you please expand the intro/abstract to compare/contrast to existing
  Bioconductor methodologies to highlight novel approaches.

The abstract and introduction have been expanded to highlight the comparison between the peptide set test and existing Bioconductor methodologies.

* [ ]  Please show an example using Bioconductor common classes for MS data.

An example using SummarizedExperiment, a common class for MS data, has been added to the vignette (Example 2).

[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.

Bioconductor utilized your github ssh-keys for git.bioconductor.org
access. To manage keys and future access you may want to active your
Bioconductor Git Credentials Account

[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: "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 Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): PepSetTest_0.99.0.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
[email protected]:packages/PepSetTest 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: b87a84a97fc0e9faa7578d274f22eb7169b1fb9c

[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): PepSetTest_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
[email protected]:packages/PepSetTest 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.

[LiNk-NY]

Hi @JmWangBio

Thank you for your submission.
Please see the review below.

Best regards,
Marcel

---

PepSetTest #3417

The main data representations in the package are matrices and data.frames.
There are a couple of functions that allow SummarizedExperiment inputs.
Should most functions support a SummarizedExperiment representation,
especially those that require a mapping data.frame?

DESCRIPTION

• Add BugReports and URL fields.
• Include your ORCID ID or remove the comment argument.

NAMESPACE

• Consider using the native pipe |> rather than %>% in magrittr
• Looks good.

vignette

• Consider wrapping the text to 80 character width for readability.
• Optional. Consider using BiocStyle::html_document
• Optional. Use bibliography: in the yaml header and include an
  inst/REFERENCES.bib file to cite your publication and direct users to
  citation(package = "PepSetTest").
• Promote safe coding practices and use seq_along(group) rather than
  1:length(group)
• Consider simplifying the code in example 3 (contrasts_res) to make it more
  reader friendly or use helper functions.

R

• Avoid using sapply and use vapply or lapply
• Avoid using eval(parse()) and use switch instead.
• Reconsider the sequence of calls in CompPepSetTest and
  EnframeContrastsRes, i.e., result %>% filter(!is.na(get(stats))). Your
  intention seems different than the code, perhaps use .[[stats]] or
  .data[[stats]].

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fdcabdf16b464e087f676c842d3546f6df3033d7

[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:
macOS 12.7.1 Monterey: PepSetTest_0.99.2.tar.gz
Linux (Ubuntu 22.04.3 LTS): PepSetTest_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
[email protected]:packages/PepSetTest to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[JmWangBio]

Hi Marcel (@LiNk-NY ),

We appreciate your detailed comments and have updated our package following your suggestions. Please see our response below:

PepSetTest #3417

The main data representations in the package are matrices and data.frames. There are a couple of functions that allow SummarizedExperiment inputs. Should most functions support a SummarizedExperiment representation, especially those that require a mapping data.frame?

Our package has three major workflows: the competitive peptide set test workflow, the self-contained workflow, and the aggregation-based limma workflow. Following your suggestion, we have made all three workflows compatible with the SummarizedExperiment representation.

DESCRIPTION

* Add `BugReports` and `URL` fields.

BugReports and URL fields have been added.

* Include your ORCID ID or remove the comment argument.

The comment argument has been removed.

NAMESPACE

* Consider using the native pipe `|>` rather than `%>%` in `magrittr`

* Looks good.

%>% in magrittr has been replaced by |> throughout the package.

vignette

* Consider wrapping the text to 80 character width for readability.

All text in the vignette has been wrapped to 80 character width.

* Optional. Consider using `BiocStyle::html_document`

BiocStyle::html_document is now used in the vignette.

* Optional. Use `bibliography:` in the yaml header and include an
  `inst/REFERENCES.bib` file to cite your publication and direct users to
  `citation(package = "PepSetTest")`.

We have included an inst/REFERENCES.bib file and updated the vignette accordingly to cite our publication.

* Promote safe coding practices and use `seq_along(group)` rather than
  `1:length(group)`

seq_along(group) is now used in the vignette.

* Consider simplifying the code in example 3 (`contrasts_res`) to make it more
  reader friendly or use helper functions.

Example 3 has been removed to improve readability.

R

* Avoid using `sapply` and use `vapply` or `lapply`

We have replaced sapply with suggested alternatives in all R scripts.

* Avoid using `eval(parse())` and use `switch` instead.

We have removed eval(parse()) from all R scripts.

* Reconsider the sequence of calls in `CompPepSetTest` and
  `EnframeContrastsRes`, i.e., `result %>% filter(!is.na(get(stats)))`. Your
  intention seems different than the code, perhaps use `.[[stats]]` or
  `.data[[stats]]`.

We have fixed this line of code by renaming the stats argument of CompPepSetTest.

Please let us know if you have any additional questions or comments.