SparseSignaturesPlus

[danro9685]

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• Repository: https://github.com/danro9685/SparseSignaturesPlus

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[bioc-issue-bot]

Hi @danro9685

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: SparseSignaturesPlus
Version: 0.99.1
Date: 2022-10-03
Title: SparseSignaturesPlus
Authors@R: c(
    person("Daniele", "Ramazzotti", role=c("cre","aut"),email="daniele.ramazzotti@unimib.it",
      comment = c(ORCID = "0000-0002-6087-2666")),
    person("Luca", "De Sano", role=c("aut"), email="luca.desano@gmail.com",
      comment = c(ORCID = "0000-0002-9618-3774")))
Maintainer: Luca De Sano <luca.desano@gmail.com>
Depends:
    R (>= 4.1.0),
    NMF
Imports:
    Biostrings,
    BSgenome,
    BSgenome.Hsapiens.1000genomes.hs37d5,
    data.table,
    GenomeInfoDb,
    GenomicRanges,
    glmnet,
    ggplot2,
    gridExtra,
    IRanges,
    lsa,
    nnls,
    reshape2
Suggests:
    BiocGenerics,
    BiocStyle,
    testthat,
    knitr,
Name:
    An R package for the the efficient extraction and assignment of mutational signatures from cancer genomes
Description:
    Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed SparseSignaturesPlus, a framework that allows the efficient extraction and assignment of mutational signatures.
Encoding: UTF-8
License: file LICENSE
URL: https://github.com/danro9685/SparseSignaturesPlus
BugReports: https://github.com/danro9685/SparseSignaturesPlus
biocViews: BiomedicalInformatics, 
 SomaticMutation
RoxygenNote: 7.2.1
VignetteBuilder: knitr

[vjcitn]

Thanks for this submission. There are already a few packages in Bioconductor addressing mutational signatures -- MutationalPatterns, SomaticSignatures, musicatk. Can you give some background on how your package adds to the toolset for analysts in this domain? Are any of the data structures in those packages -- or other Bioconductor data structures -- worth reusing in your package?

[danro9685]

Dear @vjcitn,

This package implements a new algorithm for mutational signatures analysis, which is not currently included in any of the packages you have mentioned. We will clarify this and also check for other Bioconductor packages that might be worth reusing.

Thank you.

Best, Daniele

[danro9685]

Dear @vjcitn,

We have updated the documentation as suggested. Please let us know if you have additional pre-review suggestions.

Thanks, Daniele

[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 Linux, Mac, and Windows.

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. 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/SparseSignaturesPlus to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[luca-dex]

Dear @vjcitn I'm the maintainer of the package. I already added the bioconductor remotes to our package and we're trying to push some changes but, at the moment, SparseSignaturePlus is not among the packages to which I access on git.bioconductor.org so my SSH key is not accepted.

$ git fetch --all
Fetching origin
Fetching upstream
FATAL: R any packages/SparseSignaturePlus l.desano DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: could not fetch upstream

Could you please help us in sorting out this issue?

Thanks

[lshep]

@luca-dex Bioconductor by default (and encourages) only one active maintainer. Daniele was given immediate access as that was who was listed as the maintainer in the DESCRIPTION. I have made the necessary adjustments on our end and you should have access now.

[luca-dex]

Thank @lshep , I'll wait to have SpareSignaturePlus in the list of package on BiocCredentials after it will be hopefully accepted.

@vjcitn we did the necessary updates on our github, so the issue that were highlighed by BiocCheck, should have been solved

Thanks for the support

[lshep]

@luca-dex sorry I forgot to push the changes up. You should have access now.

[nilseling]

Dear @luca-dex and @danro9685 ,

thanks for submitting the SparseSignaturesPlus package. I had a first look at the package and there are some things that need to be addressed before acceptance (see below). You are currently maintaining the SparseSignatures package and I was wondering about the motivation to create a new package rather than integrating the described functions into the existing package?

Please provide a point-by-point response to the checklist below and let me know if you have questions.

General package development

• [x] Please address the following NOTE in R CMD build:

* checking R code for possible problems ... NOTE
get.MNV.counts: no visible global function definition for ‘.’
get.SBS.counts: no visible global function definition for ‘.’
groups.CN.plot: no visible binding for global variable ‘value’
groups.CN.plot: no visible binding for global variable ‘alt’
groups.CX.plot: no visible binding for global variable ‘value’
groups.MNV.plot: no visible binding for global variable ‘Context’
groups.MNV.plot: no visible binding for global variable ‘value’
groups.MNV.plot: no visible binding for global variable ‘alt’
groups.SBS.plot: no visible binding for global variable ‘Context’
groups.SBS.plot: no visible binding for global variable ‘value’
groups.SBS.plot: no visible binding for global variable ‘alt’
patients.CN.plot: no visible binding for global variable ‘alt’
patients.CN.plot: no visible binding for global variable ‘patient’
patients.CN.plot: no visible binding for global variable ‘value’
patients.CX.plot: no visible binding for global variable ‘patient’
patients.CX.plot: no visible binding for global variable ‘value’
patients.MNV.plot: no visible binding for global variable ‘Context’
patients.MNV.plot: no visible binding for global variable ‘alt’
patients.MNV.plot: no visible binding for global variable ‘patient’
patients.MNV.plot: no visible binding for global variable ‘value’
patients.SBS.plot: no visible binding for global variable ‘Context’
patients.SBS.plot: no visible binding for global variable ‘alt’
patients.SBS.plot: no visible binding for global variable ‘patient’
patients.SBS.plot: no visible binding for global variable ‘value’
signatures.CN.plot: no visible binding for global variable ‘alt’
signatures.CN.plot: no visible binding for global variable ‘value’
signatures.CX.plot: no visible binding for global variable ‘value’
signatures.MNV.plot: no visible binding for global variable ‘Context’
signatures.MNV.plot: no visible binding for global variable ‘alt’
signatures.MNV.plot: no visible binding for global variable ‘value’
signatures.SBS.plot: no visible binding for global variable ‘Context’
signatures.SBS.plot: no visible binding for global variable ‘alt’
signatures.SBS.plot: no visible binding for global variable ‘value’

For the plotting functions you could use aes_string() instead of aes() to resolve the issue.

The DESCRIPTION file

• [x] I would recommend to move the Name field entry to the Title field entry and remove the Name field.
• [x] The parallel package is missing in Imports
• [x] It is not necessary to define the R version in Depends but if you do, please update it to the current release (4.2.0)
• [x] I would recommend to change the BugReports field to BugReports: https://github.com/danro9685/SparseSignaturesPlus/issues

The NAMESPACE file

• [x] Please use camelCase or snake_case for function names and avoid the use of . as this indicates a method in the S3 class system.
• [ ] Selectively import the needed functions via @importFrom instead of importing the whole package via @import. Also make sure that you specifically import functions rather than calling them via pkg::function within the code.

The NEWS file

• [x] The package version in the NEWS.Rd file does not match the package version in DESCRIPTION.

Package data

• [ ] For the user it might be nice to see where the data can be accessed online. You could consider adding a link to the original data repository.

Documentation

Vignette

• [x] From the vignette it is not clear how the signatures are computed. Please add more details on the actual approach especially considering that there is currently no manuscript linked in the vignette.
• [x] The vignette states that SparseSignaturesPlus supports different types of mutational signatures including MNV, CX, and CN. If this is part of the functionality of SparseSignaturesPlus it should also be highlighted in the vignette. Looking at the man pages I did not find information on how to compute the different types of signatures.
• [x] It is recommended to provide the vignette in .Rmd format using BiocStyle. I would propose to merge the 2 .Rmd vignettes that you already have so that your vignette contains an Introduction section and use BiocStyle for formatting. The name of the vignette could be SparseSignaturesPlus.Rmd as currently the .Rnw vignette can only be accessed via vignette("vignette") in R. Please refer to the vignettes section for more info.
• [x] The package name indicates that SparseSignaturesPlus is a follow-up package to SparseSignatures. In the Introduction of the vignette, please refer to SparseSignatures and how the current package is different. In this context you can motivate the inclusion of SparseSignaturesPlus into Bioconductor.
• [x] Please add an Installation section to the vignette highlighting the Bioconductor installation instructions in an eval=FALSE chunk.
• [ ] You could consider refering to existing packages that compute mutational signatures and how they differ from SparseSignaturesPlus.

Man pages

• [x] It is recommended to add a package-level man page which can be accessed via ?SparseSignaturesPlus.
• [x] At least 80% of man pages documenting exported objects must have runnable examples. Please add examples to the functions that currently don't contain any.

Unit tests

• [ ] Please consider adding unit tests covering the main functions of your package.

SparseSignaturesPlus Coverage: 0.00%
R/data.import.R: 0.00%
R/mutational.signatures.discovery.R: 0.00%
R/mutational.signatures.significance.R: 0.00%
R/visualization.R: 0.00%

R code

• [ ] Please address the following errors flagged by BiocCheck. In general it is not recommended setting a seed within but rather directly before calling the function.

* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* NOTE: Avoid using '=' for assignment and use '<-' instead
* WARNING: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes
* WARNING: Remove set.seed usage (found 4 times)
* WARNING: Avoid the use of 'library' or 'require' in R code

• [ ] Please add validity checks for all function arguments.
• [ ] It is recommended to use BiocParallel for parallelisation. The way you set up parallelised computations appreas quite complex and using BiocParallel might help with that.
• [x] It is recommended to indicate non-exported functions with a . prefix.
• [x] I would recommend to unquote function names.
• [ ] Some lines such as the one below are difficult to parse. It is recommended to shorten them by creating input variables before the function call and by adding line breaks.

res <- cv.glmnet(cbind(t(curr_beta_values),matrix(rep(0,ncol(curr_beta_values)),ncol=1)),as.vector(x[j,]),type.measure="mse",nfolds=10,nlambda=10,family="gaussian",lower.limits=0.00)

[danro9685]

Dear @nilseling,

Thanks for your very detailed review of our package.

We have just pushed on the GitHub page of the tool changes addressing: (i) all your points for "General package development", "The DESCRIPTION file" and "The NAMESPACE file" and (ii) most of your points for "Documentation" and "R code". We are taking care of the remaining things as soon as possible.

In the mean time, we wanted to ask your advice regarding the package name. This tool (SparseSignaturesPlus) implements a new algorithm for mutational signatures analysis. The related paper is in preparation and will be referred in the package as soon as it is ready, but we don't think this will happen by the next Bioconductor release. To this end, besides providing details on the algorithm, do you think it would make sense to also change the package name? Maybe this would reduce the confusion regarding the already published SparseSignatures algorithm, from which SparseSignaturesPlus takes some inspiration, but the two methods are different.

Please let us know your thoughts. Thanks, Daniele and @luca-dex

[nilseling]

Hi @luca-dex and @danro9685

I would then propose to change the name of the package to avoid confusion. If you agree with this I will close this issue and wait for you to open a new issue with the new name (see package name for guidance). We will then fast track the issue and I will continue with the review where we left off here. Does that sound alright?

[danro9685]

Dear @nilseling,

This sounds great, as new name, what about: RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization). If this is good, we can proceed as you suggested.

Thanks, Daniele and Luca

[nilseling]

Sounds good. I had a quick check with available("RESOLVE") and the name seems to be alright. I will close this issue now - please open a new issue using RESOLVE

[danro9685]

Dear @nilseling I have opened the issue for the new package. Please add @luca-dex as primary maintainer of the package. Thanks!