MWASTools

[AndreaRMICL]

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[bioc-issue-bot]

Hi @AndreaRMICL

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: MWASTools
Type: Package
Title: MWASTools: an integrated pipeline to perform metabolome-wide association studies
Version: 0.99.0
Date: 2016-06-27
Author: Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13@imperial.ac.uk>, Joram M. Posma <j.posma11@imperial.ac.uk>, Rafael Ayala <r.ayala14@imperial.ac.uk>, Ana L. Neves <ana.luisa.neves14@imperial.ac.uk>, Jeremy K. Nicholson <j.nicholson@imperial.ac.uk>, Marc-Emmanuel Dumas <m.dumas@imperial.ac.uk>
Maintainer: Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13@imperial.ac.uk>, Rafael Ayala <r.ayala14@imperial.ac.uk>
Description: MWAS provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY.
License: CC BY-NC-ND 4.0
Depends: R(>= 3.3)
Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
VignetteBuilder: knitr
Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, graphics, stats, utils
biocViews: Metabolomics, Lipidomics, Cheminformatics, SystemsBiology, QualityControl
NeedsCompilation: no
LazyData: true
Encoding: UTF-8

[lawremi]

Needs to be based on SummarizedExperiment. The assay matrix and clinical variables would fit nicely in one.

[AndreaRMICL]

Hi @lawremi,

Thanks for your message. Do you mean creating SummarizedExperiment object using the datasets metabolic_data and clinical_data that I use for the vignette and for the examples of the help files ?

Thanks,

Andrea

[lawremi]

Sure, but the main thing is that the package itself (the API, even the implementaton) is based on it. It should expect a SummarizedExperiment as input, for example.

[AndreaRMICL]

I think we could only use SummarizedExperiment in the function MWAS_stats () as it is the only function of the package where the metabolic data and the clinical data are used together. However, wouldn´t it be easier for the users to input the metabolic and clinical data as separate variables ?

[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.

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 following build report for more details:

http://bioconductor.org/spb_reports/MWASTools_buildreport_20161020154326.html

[lawremi]

I would think users would appreciate a SummarizedExperiment interface, even for functions that do not require all of the information, because they will already be using such an object in their workflow. It should also simplify your implementation, since it can now make assumptions about the consistency of the data components.

[AndreaRMICL]

Thanks @lawremi I will start looking at it in detail soon.

[AndreaRMICL]

Hi @lawremi,

Thanks very much for your advice. Actually it is really useful to use the SummarizedExperiment interface. I'm now modifying the functions so that the package is all based on a SummarizedExperiment. I'll push the updated version of the package hopefully tomorrow.

Andrea

[bioc-issue-bot]

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

288e62f v 0.99.1

[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 following build report for more details:

http://bioconductor.org/spb_reports/MWASTools_buildreport_20161024122411.html

[lshep]

Thank you for transitioning to the SummarizedExperiment object. This will greatly improve its compatibility with existing Bioconductor packages. Please see the additional comments below. Once you are done updating, please respond back here with a summary of what was changed or any justification or responses to the issues.

Vignette/R code:

• [ ] Please add installation instructions from Bioconductor.

source("http://www.bioconductor.org/biocLite.R")
biocLite("MWASTools")

• [ ] There is a missing reference in section 3.2
• [ ] You shouldn't need to load SummarizedExperiment since it is listed in the DESCRIPTION and NAMESPACE.
• [ ] Will the metabolic data be a frequently accessed slot. if so should there be a accessor method for the metabolic data so instead of t(assays(metabo_SE)$metabolic_data) it could just be something like metabolicData(metabo_SE)?
• [ ] what is the reasoning behind having static png images and using eval=FALSE for the code that would generate these images? we generally like graphs/plots generated interactively.
• [ ] You define some "needed variables" like metabo_matrix, ppm, ref_spectrum and then use in the functions like QC_CV, QC_CV_specNMR, MWSA_skylineNMR. Would the desired data change in these variables or can these actually be calculated from within the function to save users steps? The same with STOCSY_NMR, why couldn't your main metabo_SE object be used as input instead of having to calculate metabo_matrix and ppm?

man:

the same as vignette, you shouldn't need to separately load the SummarizedExperiment library as you import it as part of your package.

Thank you for your submission. I look forward to your responses.

[AndreaRMICL]

Hi @lshep,

Thanks very much for your feedback and for helping us to improve our package. I've just pushed an updated version, but by mistake I wrote version 0.99.3, instead of 0.99.2, I'm not sure if this is a problem.

See some comments below:

1) Vignette/R code:

-We've added installation instructions from Bioconductor. -We've added the missing reference in 3.2 (now 4.2). -We've modified the code so that "metabo_SE" is the input argument for "STOCSY_NMR()", "QC_CV_specNMR()" and "MWAS_skylineNMR()". Now the variables "metabo_matrix" and "ppm" are generated internally from the "metabo_SE" variable. That was a very good suggestion, I like it much better like this (thanks!). -We decided to include static images in the vignette because we think the size of the static images looks much nicer than if the images are generated interactively. I just wonder if there is a good way to customize the dimensions of the images interactively ? We tried with "dev.new()" but it did not really work.

2) man:

-In the example for : "MWAS_SummarizedExperiment()", I extracted the individual elements of metabo_SE, to illustrate the functionality of the function. To do so, I need to use the function "assays()" from the SummarizedExperiment package, and this is why I need to do library(SummarizedExperiment).

Thanks very much,

Best wishes,

Andrea

[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 following build report for more details:

http://bioconductor.org/spb_reports/MWASTools_buildreport_20161107152553.html

[bioc-issue-bot]

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

ae253a1 v.0.99.4

[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: "ABNORMAL". 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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http://bioconductor.org/spb_reports/MWASTools_buildreport_20161116110315.html

[bioc-issue-bot]

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

67eca8b v.0.99.5

[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 following build report for more details:

http://bioconductor.org/spb_reports/MWASTools_buildreport_20161116112020.html

[bioc-issue-bot]

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

3756831 v.0.99.6

[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.

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[bioc-issue-bot]

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

79e3f89 v.0.99.7

[bioc-issue-bot]

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

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

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[bioc-issue-bot]

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

06d50b2 v.0.99.8

[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.

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[lshep]

It is looking very close to acceptance. The limiting factor right now is the package size. We generally only accept packages that are >4Mb.

There are two options:

1. reduces the size of the data objects being utilized
2. If you get rid of the static .png in the vignette that should put you under as well. I know you mentioned the images looked nicer when static rather than generating interactively. Have you tried specifying the plotting region width and length in the .Rmd code chunk? When you specify a code chunk for plotting you can use the arguments fig.height and fig.width to change the defaults.

Lori

[AndreaRMICL]

Hi @lshep,

Thanks very much for your reply. I don't understand why when saving the data as a SummarizedExperiment object, the size of the package increased.... But anyway, I am going to try to reduce a bit the resolution of the NMR spectra of the example dataset, and see if this helps.

Best wishes,

Andrea

[bioc-issue-bot]

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

4887126 v.0.99.9

[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/MWASTools_buildreport_20161117172151.html

[AndreaRMICL]

Hi @lshep,

I've now reduced the size of the data objects, so I think that now the package meets the size requirements. Let me know if there are further changes to be made.

Best wishes,

Andrea

[bioc-issue-bot]

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

96de6c3 v.0.99.10

[AndreaRMICL]

Hi @lshep,

I have also included your suggestion about changing the dimensions of the figure in the .Rmd code chunck, so now the figures are created interactively. Thanks for the suggestion!

Andrea

[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/MWASTools_buildreport_20161118030204.html

[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/MWASTools_buildreport_20161118093239.html

[lshep]

Thank you. Everything else looked good. I will mark your package as accepted and you should receive svn instructions via email soon. Please keep the issue open; we will close it when we send you credentials.

[AndreaRMICL]

Thanks very much for all your help to both @lshep and @lawremi for your contributions to our package! Best,

Andrea

[AndreaRMICL]

Hi @lshep, I was wondering if my package will be included in Bioconductor this week, or later on. I'm about to submit a paper where I have use the package, so it would be great if I could cite it from Bioconductor.

Thanks very much, Andrea

[lshep]

Hi @AndreaRMICL I'll double check on your svn credentials with @mtmorgan . As soon as you are sent the credentials you will be able to include your package in the devel version of Bioconductor.

[AndreaRMICL]

Thanks very much @lshep

[AndreaRMICL]

Hi @lshep,

Sorry to bother you again with this. I was just wondering if you have any news about the status of my package.

Thanks very much in advance,

Best wishes,

Andrea