SplicingFactory

[peterszikora]

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[bioc-issue-bot]

Hi @peterszikora

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: SplicingFactory
Type: Package
Title: Splicing Diversity Analysis for Transcriptome Data
biocViews: Transcriptomics, RNASeq, DifferentialSplicing, AlternativeSplicing, TranscriptomeVariant
Version: 0.99.0
Authors@R: c(
    person("Peter A.", "Szikora", role = c("aut", "cre"), email = "peter.andras.szikora@gmail.com"),
    person("Endre", "Sebestyen", role = "aut", email = "sebestyen.endre@med.semmelweis-univ.hu", comment = c(ORCID = "0000-0001-5470-2161")))
Description: The SplicingFactory R package uses transcript-level expression
    values to analyze splicing diversity based on various statistical measures,
    like Shannon entropy or the Gini index. These measures can quantify
    transcript isoform diversity within samples or between conditions.
    Additionally, the package analyzes the isoform diversity data, looking for
    significant changes between conditions.
RoxygenNote: 7.1.0
Imports: methods, stats, Biobase, ggplot2, tidyr
Suggests:
    testthat,
    knitr,
    rmarkdown
Depends: R (>= 4.0)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr

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[bioc-issue-bot]

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[mtmorgan]

Please update your package to use SummarizedExperiment rather than ExpressionSet.

[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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

a71102a Version bump

[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.

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[LiNk-NY]

Hi @peterszikora ,
Any updates on using SummarizedExperiment?
Thanks.

[peterszikora]

Hi, thank you for the comment, working on it.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

5886bb9 SummarizedExperiment input type instead of Express...

[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.

[esebesty]

Hi @mtmorgan and @LiNk-NY

We were discussing the right way to use SummarizedExperiment and were curious about your opinion. Right now, the package deals with data where we have a single table with samples as columns and transcripts as rows. However, SummarizedExperiment might contain more than one assay with a matrix-like representation of read counts, etc. We don't want to simply pick the first assay for further analysis, so we were wondering what to do.

• Just pick the first assay, or an assay with a specific name.
• Implement some parameter for the calculate_diversity function, to specify the assay to be analyzed.
• Loop over the entire SummarizedExperiment object, process all tables, and return a list of data frames. This would mean additional complications in downstream analysis too.

Initially we decided to use ExpressionSet as similar tools, doing differential expression, like limma also use ExpressionSet. voom and lmFit of limma both expect a matrix-like data object.

[LiNk-NY]

Hi Endre, @esebesty

I think the best option would be to include an argument ('parameter') in the calculate_diversity
function with default of 1 for the first assay in the SummarizedExperiment. The user will also
have the option to change the argument to their liking.

Using these tools (limma etc.) should be separate from the functionality and data representation
you provide. Ideally, these tools would accept a SummarizedExperiment as input. The
responsibility then falls on the analyst to provide the correct input for these tools. They would have
to use assay(SE) to get the matrix data.

I hope this answers your questions.
Best,
Marcel

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

58099c2 SummarizedExperiment updated

[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.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

[peterszikora]

@mtmorgan and @LiNk-NY

Thank you again for your comments, we updated the package with SummarizedExperiment, waiting for your detailed review.

[LiNk-NY]

Hi @peterszikora

Thank you for your submission.
Please see the review below.
If you have any questions, continue the thread here.

Best,
Marcel

---

SplicingFactory #1517

DESCRIPTION

• Looks good

NAMESPACE

• Looks straightforward

vignettes/

• Looks good

R

• Use is.matrix and is(x, "SummarizedExperiment") type of methods
  for obtaining the class of the input object.
• Use a verbose argument for all the messages in calculate_diversity
  and other functions
• User-facing functions should allow a SummarizedExperiment input
  (calculate_method, calculate_diversity, etc.) and ideally return a
  SummarizedExperiment
• Allow for alternative correction methods in wilcoxon. Is BH the only
  correction method? It seems to be hard-coded.
• Should calculate_*entropy and related functions be exported and work on
  a SummarizedExperiment object?
• Bothcalculcate_entropy and calculate_laplace_entropy look about the same,
  perhaps make them into one function with a type argument so that you're
  re-using code?

data

• Rename the dataset example_dataset into something more descriptive
• If possible, re-use data from an existing TCGA data resource (or even
  GenomicDataCommons)

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

49fe913 Example dataset and formatting updates
3901973 Bug and formatting corrections, verbose parameter ...

[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/SplicingFactory 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; starting a build. Commits are:

fcc3ea5 SummarizedExperiment and vignette updates

[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, skipped".
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/SplicingFactory to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

This issue is being closed because there has been no progress
for an extended period of time. You may reopen the issue when
you have the time to actively participate in the review /
submission process. Please also keep in mind that a package
accepted to Bioconductor requires a commitment on your part to
ongoing maintenance.

Thank you for your interest in Bioconductor.

[esebesty]

Please reopen the issue, we are (hopefully) done with all necessary changes.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

c942c59 Minor correction and github actions update

[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: "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. 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/SplicingFactory 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; starting a build. Commits are:

c88017f R version update

[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.

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

[LiNk-NY]

Hi Endre, @esebesty
Thank you for making those changes. I had a look at the package and it looks good.
I'm accepting it.
Best regards,
Marcel

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[mtmorgan]

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