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msImpute #1606

Closed soroorh closed 3 years ago

soroorh commented 4 years ago

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bioc-issue-bot commented 4 years ago

Hi @soroorh

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: msImpute
Type: Package
Title: Imputation of label-free mass spectrometry peptides
Version: 0.99.0
Authors@R: 
    person(given = "Soroor",
 family = "Hediyeh-zadeh",
 role = c("aut", "cre"),
 email = "hediyehzadeh.s@wehi.edu.au",
 comment = c(ORCID = "0000-0001-7513-6779"))
Description: MsImpute is a package for imputation of peptide intensity in proteomics experiments.
    It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability 
    distribution of the data post imputation.  Currently, msImpute completes missing values by low-rank approximation of the underlying 
    data matrix.
Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats
License: GPL (>=2)
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/DavisLaboratory/msImpute/issues
RoxygenNote: 7.0.2
Suggests: BiocStyle, knitr, rmarkdown, limma, ComplexHeatmap, imputeLCMD, tidyr
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Software
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bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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Kayla-Morrell commented 4 years ago

Hello @soroorh,

Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be but we strongly encourage them. Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

NAMESPACE

NEWS

Data

Vignette

Man pages

Unit tests

R code

Best, Kayla

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

Dear Package contributor,

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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 git@git.bioconductor.org:packages/msImpute to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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Your package has been built on Linux, Mac, and Windows.

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soroorh commented 4 years ago

Hello @Kayla-Morrell ,

Thank you for your instructions. Please see below.

DESCRIPTION

  • [x] REQUIRED: File LICENSE is not mentioned in the DESCRIPTION file. The LICENSE file should be removed since you are using a standard library.
  • [x] REQUIRED: There should be 'SystemRequirements:' defined if users of the package need python to run certain functions.

NAMESPACE

  • [x] REQUIRED: Internal functions should not be exported.

NEWS

  • [x] REQUIRED: The versioning is incorrect in your NEWS file.

Data

  • [x] REQUIRED: The raw data should not be accessed from github. We would rather have the data be part of the package or as a seperate data package. When the data is hosted on github, there is no gaurantee that the data will always be accessible to users, that it won't move, etc.

The vignette now mentions the name of the public repository where the raw data can be downloaded. This should address your concerns around accessibility of the data. The link to these public repositories are also documented in the data man pages.

Vignette

  • [x] REQUIRED: Is there a difference between 'msImpute-vignette.Rmd' and 'usersguide.Rnw'? If there are multiple vignette files, each should demonstrate a unique function of the package.

Yes, there is. The intention is to accompany the package with a users guide, similar to thelimma package which comes with a static, pre-compiled pdf document that is also very comprehensive. The package vignette 'msImpute-vignette.Rmd' covers most of the functions, and demonstrates that the functions run successfully. The users guide is intended to be more comprehensive and detailed and covers all functions implemented in the package. The idea is to help users with using the tools implemented in the package, and assist them in interpreting the results returned by the functions . We are treating the pdf file as a static image, if you wish. The Rnw file just embeds the pdf into the second vignette file. So, there is one dynamic vignette (.Rmd) and one static users guide which is created when the Rnw file is compiled.

  • [x] REQUIRED: Only the vignette files (.Rnw or .Rmd) and any necessary static images should be in this directory. Please remove the .pdf file.

I explained the intention of having the pdf file above. This is just a solution to make a users guide available that can be accessed from the landing page, as limma does.

  • [x] REQUIRED: The processing of the raw data should be included in an 'inst/scripts/' directory and not in the vignette. The data used in the vignette should be the data provided in the package (pxd01477, pxd007959, and pxd010943).

The data used in the vignette are indeed the data provided in the package. The corresponding codes for processing of raw data are now removed from the vignette. The users are instead advised to consult the users guide for detailed description of data processing.

  • [x] REQUIRED: The vignette must include executable code. Static vignettes are not acceptable. Reduce the amount of eval=FALSE in the vignette since these undermine the benefit of vignettes.

Man pages

  • [x] REQUIRED: Only exported functions should be documented. For documentation of internal functions you can add @keywords internal which will remove the function from the documentation index.

Unit tests

R code

  • [x] REQUIRED: Clarify how 1 object is initialized.
    • function (object) gromov_wasserstein (gw)
  • [x] REQUIRED: Avoid sapply(); use vapply(). Found in files:
    • computeStructuralMetrics.R, line 114
  • [x] REQUIRED: Avoid 1:...; use seq_len() or seq_along(). Found in files:
    • computeStructuralMetrics.R, lines 155 and 156
    • KNC.R, line 38
    • KNN.R, line 30
    • selectFeatures.R, lines 80 and 90
  • [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 302 lines that are > 80 characters long.
  • [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 246 lines that are not.

Much appreciated, Soroor

soroorh commented 3 years ago

Dear @Kayla-Morrell ,

I believe the package is ready for a re-review. Many thanks, Soroor

Kayla-Morrell commented 3 years ago

Hello @soroorh - Thank you for making the necessary changes above. However, I don't feel that you addressed the point about the data being available for download from GitHub. As stated in our data guidelines here, the raw data needs to be included in the package itself or should be a separate data package if the files are too large. Please address this issue.

Best, Kayla

soroorh commented 3 years ago

Dear @Kayla-Morrell,

Thank you for your help with the package.

The users do not have to download any data from GitHub to run package examples and vignettes. All the required data is included in the package. The package examples use calls to data() as they are now, and can't be changed. Even if I create a ExperimentHub package for the raw data, that is not to the interest of msImpute, as it requires the data in the format loaded via data() call. The link to the source though is documented in the man pages, as demonstrated below. Would this help addressing your concerns @Kayla-Morrell ?

Here is a data man page as a proof of concept that link to direct download from sources (not github) is provided

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/pxd007959.R
\docType{data}
\name{pxd007959}
\alias{pxd007959}
\title{Processed peptide intensity matrix and experimental design table from PXD007959 study}
\format{
A list of two: samples (data frame of sample descriptions), and y (numeric matrix of peptide intensity values)
}
\source{
\url{http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD007959}
}
\usage{
pxd007959
}
\description{
Extracellular vesicles isolated from the descending colon of pediatric patients with inflammatory bowel disease
and control patients. Characterizes the proteomic profile of extracellular vesicles isolated from the descending colon
of pediatric patients with inflammatory bowel disease and control participants. This object contains data from peptide.txt
table output by MaxQuant. Rows are Modified Peptide IDs. Charge state variations are treated as distinct peptide species.
Reverse complements and contaminant peptides are discarded. Peptides with more than 4 observed intensity values are retained.
Additionally, qualified peptides are required to map uniquely to proteins.
Two of the samples with missing group annotation were excluded.
The peptide.txt and experimentalDesignTemplate files can be downloaded as RDS object from \url{https://github.com/soroorh/proteomicscasestudies}.
Code for data processing is provided in package vignette.
}
\references{
Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, Mayne J, Cheng K, Liao B, Li L, Singleton R, Mack D, Stintzi A, Figeys D, Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nat Commun, 9(1):2873(2018)
}
\keyword{datasets}

Best,

Soroor

soroorh commented 3 years ago

also, @Kayla-Morrell , as per this statement in the data guidelines:

If existing data is not available or applicable, or a new smaller dataset is needed for examples in the package, data can be included either as a separate data package (for larger amounts of data) or within the package (for smaller datasets).

we indeed just needed a new smaller dataset for package examples and the vignette, which are included in the package (pxd01477, pxd007959, and pxd010943). The guidelines state that a traditional package is still acceptable:

Bioconductor encourages creating an experiment data package that utilizes ExperimentHub or AnnotationHub (See Creating an Experiment Hub Package or Creating an Annotation Hub Package) but a traditional package that encapsulates the data is also okay

Does this help?

Many thanks, Soroor

soroorh commented 3 years ago

Dear @Kayla-Morrell , Can you please point me to the section of the data guidelines that you are referring to, please? the guidelines under Raw Data and the inst/extdata/ Directory states that it is desirable

It is often desirable to show a workflow which involves parsing or loading of raw files

My understanding is that there are 4 principal practices for including data (corresponding to the 4 headings under Including Data, and exported data in data/ is one of them. My apologies, I am confused!

Many thanks, Soroor

soroorh commented 3 years ago

@Kayla-Morrell - can you please help me with clarifying your expectation re: raw data? thanks heaps!

mtmorgan commented 3 years ago

@soroorh please take a deep breath; Kayla, like each of us, has many obligations to fulfill, and yours is only one.

From my reading of your issue, it seems like the data() is consistent with our policies.

I personally would discourage your inclusion of the static vignette -- although limma does an excellent job of this, our experience is that static vignettes quickly become 'pictures of code' that fail because the code in the vignette no longer functions as illustrated. Of course you intend to maintain your code, but our experience has really been that best intentions are often not realized. I would encourage you to remove the static vignette from your package; perhaps reference it from your dynamic vignette. I think this would help to address Kayla's concerns, because you make reference, in both vignettes, to data in your github repository, and such data is not appropriate for use in a Bioconductor package.

soroorh commented 3 years ago

Thank you @mtmorgan . This is all I needed to understand to address her concerns. I definitely appreciate how busy all reviewer's are, and appreciate their time and assistance. I tend to receive comments every 14 days for this issue, and was worried I have to wait another 14 days for this clarification. I shall address your concerns now. many thanks

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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 git@git.bioconductor.org:packages/msImpute to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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