mpra

[lmyint]

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

• Repository: https://github.com/hansenlab/mpra

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[bioc-issue-bot]

Hi @lmyint

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: mpra
Version: 0.99.0
Title: Analyze massively parallel reporter assays
Description: Tools to analyze & visualize massively parallel report assays (MPRA).
Authors@R: c(
       person("Leslie", "Myint", role = c("cre", "aut"), email = "lmyint1@jhu.edu"),
       person(c("Kasper", "D."), "Hansen", role = "aut"))
Depends:
    R (>= 3.4.0),
    methods,
    BiocGenerics,
    SummarizedExperiment,
    limma
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    RUnit
Imports:
    S4Vectors,
    scales,
    stats,
    graphics,
    statmod
Collate:
    mpra_set.R
    utils.R
    fit.R
VignetteBuilder: knitr
License: Artistic-2.0
URL: https://github.com/hansenlab/mpra
BugReports: https://github.com/hansenlab/mpra/issues
biocViews: Software, GeneRegulation, Sequencing, FunctionalGenomics

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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 following build report for more details:

http://bioconductor.org/spb_reports/mpra_buildreport_20171004111006.html

[lmyint]

Thanks for taking a look, Michael. Which functions were you referring to? The only place where we have specific processing for the cited publication (Inoue) is in inst/scripts where we create the example data. Otherwise the functions that we export are related to general purpose analysis for any experiment. This is predicated on users to creating the MPRASet object themselves though as we explain in the first section of the vignette. We have set it up this way because data from these experiments often come in a series of text files with no prescribed formatting, columns, etc.

[lawremi]

Sorry, I meant to post that on a different issue but now I have no idea which one it was, because there are so many in play. I'll delete my comment.

[mtmorgan]

Sorry I meant to post these brief comments earlier; your package looks really good, if you can make the changes outlined below in the next few days I will try to add it in time for the release at the end of October.

DESCRIPTION

• provide a more descriptive Description: so that users can figure out the relevance of this package to their needs.

vignettes

• looks good

R

• fit.R:8 use match.arg(model_type) for validation

• generally: spend more time validating inputs, especially to top-level functions, to avoid complicated or subtle errors later.

• mpra_set.R:39 the show() method seems to be a no-op, remove?

• utils.R:3 using stop() with sprintf() is redundant; stop() does the equivalent of paste() internally.

man

• good!

• mpralm.Rd:14 provide some additional detail on need for agreement between dimensions of object and design.

[lmyint]

Hi Martin, Thank you for the feedback. We have made the changes that you've suggested above, and bumped the version a few times, each without a triggered rebuild. With each push, I see that the webhook has a 404 error, so I'm not sure if something is down with the build system.

The specific changes we made include

• DESCRIPTION: the Description field has been updated to indicate the specific pieces of functionality provided.
• fit.R:8 use match.arg(model_type) for validation
• Validating inputs: added checking of object type in several functions and dimension concordance in the functions in fit.R
• show(): we included information about the existence of barcode information, which is useful to users who want to know if their data may have been aggregated already
• utils.R: updated stop()
• mpralm.Rd: expanded description for design to detail need for dimension agreements

[bioc-issue-bot]

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

eee2a1b Bump version

[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 following build report for more details:

http://bioconductor.org/spb_reports/mpra_buildreport_20171020131946.html

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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See further instructions at

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for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using biocLite(\"mpra\"). The package 'landing page' will be created at

https://bioconductor.org/packages/mpra

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.