PepSetTest

[JmWangBio]

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[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", , "jmwang.bio@gmail.com", 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).

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