DEP

[arnesmits]

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• Repository: https://github.com/arnesmits/DEP

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[bioc-issue-bot]

Hi @arnesmits

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: DEP
Title: Differential Enrichment analysis of Proteomics data
Version: 0.99.0
Authors@R: c(
    person("Arne", "Smits", email = "arne.smits@embl.de", role = "cre"),
    person("Wolfgang", "Huber", email = "winston@rstudio.com", role = "aut"))
Description: This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment.
    It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant.
    Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins.
    It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation.
    Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations.
    For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report.
    Even easier to use are the interactive Shiny apps that are provided by the package.
License: Artistic-2.0
Depends: R (>= 3.4)
Encoding: UTF-8
LazyData: true
Imports: ggplot2,
    dplyr,
    purrr,
    readr,
    tibble,
    tidyr,
    broom,
    Biobase,
    SummarizedExperiment,
    MSnbase,
    limma,
    vsn,
    fdrtool,
    ggrepel,
    ComplexHeatmap,
    RColorBrewer,
    circlize,
    shiny,
    shinydashboard,
    DT,
    rmarkdown,
    assertthat,
    gridExtra,
    BiocStyle,
    grid,
    stats,
    utils
RoxygenNote: 6.0.1
Suggests: testthat,
    knitr
biocViews: Proteomics, MassSpectrometry, DifferentialExpression
VignetteBuilder: knitr

[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/DEP_buildreport_20170801114045.html

[bioc-issue-bot]

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

284ec59 Version 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.

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/DEP_buildreport_20170810040905.html

[mtmorgan]

DESCRIPTION

• Consider wrapping long lines to 80 columns

• Carefully consider the long list of Imports: as each dependency increases the susceptibility of your package to other changes.

• Consider addtional biocViews terms

vignette

• line 42: Is setInternet2() needed?

• 109: adopt consistent use of pipes, e.g., no . as arguments here.

• The vignette looks really good, thanks!

R

• stop(paste(.)) constructs (e.g., functions.R:29) can often be replaced by stop(.).

• consider more stringent assertions, e.g., for length and non-NA values.

• For arguments such as meode (functions.R:224) consider specifying alternatives in the function signature and using match.arg() for validation.

• create local variables, e.g., idx <- is.na(assay(se)) to avoid repeated calls; also consider the optimization assay(., withDimnames = FALSE) to suppress expensive (for large assays) addition of dim names.

• functions.R:346 rowsum() on t(assay(.)) may be a more straight-forward way of calculating per-group values

• functions.R:441 and elsewhere: use seq_len() or seq_along() instead of 1:n to avoid problems when n == 0. rnorm() can take vectors of mean and sd, so probably this iteration can be replacced by a single vectorized call.

• functions.R:533 typo: "run impute() with..."

• functions.R:643: maybe as a 'too cute' expression, consider revising to apply(combn(condtions, 2), 2, paste, collapse = " - ")

• functions.R:936: use consistent indenting; the formatR or lintr package might be helpful.

• run_app_function.R: assert that app is a scalar character, else the if statement will fail in a cryptic way.

• I believe that 'best practice' in the tidyverse, in package code, is to use the _ (e.g., select_() rather than select()) form of verbs, and hence avoid the need non-standard evaluation and for utils::globalVariables(). I am not completely sure of this.

man

• Generally good. Consider using language to describe parameters using R terminology and specifying length and other constraints, e.g., add_rejections.Rd:14 \item{alpha}{numeric(1), sets the ....

inst/shiny_apps

• e.g., inst/shiny_apps/TMT/:210: be sure to avoid too much code in the app, which is not subject to R CMD check; instead, write functions accessible (maybe not exported) in the R/ directory. Ideally, the app.R file will contain the minimum code to connect server-side functionality to the implementation, without any implementation itself.

• pay attention to code formatting in these files, especially avoiding long therefore hard to parse lines

Other

• inst/NEWS: be careful to keep this accurate and in a format that can be parsed by utils::news().

• nice to see the relatively extesive tests!

[bioc-issue-bot]

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

7b95b68 wrap longer lines 7b76806 update plot_cor e8686cf update manual 3f35fbc bioc review edits 6ddb7ff update manuals 9a25522 bioc review edits ec5d840 new examples bf68078 new examples 7a623a6 less imports/dependencies a0e7051 remove GFPip example data 4f34149 remove GFPip example data a785379 add shiny and wrapper functions 399cd4e fix gather issue and edit manuals 0b8d4c9 edit manuals 1cccb1c downsize vignette 277919a reduce imports be66e25 new NEWS file d432f13 update example 4eb07cc add local variables and update examples 88bc4a8 add plot_p_hist function 4022044 both p.val and p.adj volcano plots e6f2be6 add p.val and p.adj volcano plot functions 2ccb8d1 add p_val_hist function fafbfcb update manual add links to other DEP functions dcde0db add text on prerequisites of SE 37b4a8d adapt tests 84fd742 Bioc resubmission edits 3c03613 additional unit tests 083e2a1 Bioc review c3f77d8 Bioc resubmission edits a4ceab5 DEP 0.99.2

[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/DEP_buildreport_20170825080448.html

[arnesmits]

Dear Martin,

Thank you for your review! I have carefully read your comments, edited appropriate parts of the package and pushed the changes. The edits include the following points:

Description 1) Wrapped longer lines in the description. 2) Carefully checked the Imports list and could only reduce it minimally. The package utilizes many functionalities from other packages, requiring them to be imported. 3) Additional biocViews (“DataRepresentation”) added.

Vignette 4) Implemented consistent use of pipes, thank you for noticing! 5) setInternet2() indeed does not seem to be necessary, so line 42 is deleted.

R 6) The paste() functions are removed from the stop() constructs. 7) More stringent assertions are implemented, checking for argument lengths in most functions and non-NA values in some functions. 8) Arguments with fixed alternatives are now indicated in the function signature and are checked with match.arg(). Thanks for pointing out this neat solution! 9) Implemented novel local variables to avoid repeated calls, especially those for accessing rowData and colData. 10) Thank you for noting the combination of rowsum() and t(assay(.)). Eventually, I did not implement it, because the current construct allows easy filtering based on dplyr. 11) Seq_len() is implemented in the appropriate parts. 12) functions.R:484 - originally functions.R:441 Although rnorm can take vectors of mean and sd, it cannot take a vector of the numbers of observations (if a vector is applied, it will take its length as the number of observations). Because we need different numbers of observations for the different samples, it looks like this cannot be simplified in a single vectorized call. 13) Typo is corrected. 14) Implemented paste() directly into the apply function. 15) The tidyverse indeed used to work with underscore suffixed verbs, but these are currently deprecated (dplyr >= 7.0.0).

man 16) Manuals have been edited to inform users about the class and length of parameters.

inst/shiny_apps 17) Appropriate parts of the shiny apps are reformatted (reducing long lines) and several internal (i.e. not exported) functions are implemented. This leaves the apps with only minimal implementation.

Other 18) New ‘NEWS.Rd’ file added, which can be appropriately parsed. I am looking forward to your response.

Kind regards, Arne

[mtmorgan]

Thanks for the changes and response; this looks great and I am accepting the package. We will work through adding it to the Bioconductor git repository; you should be updated in a day or so.

[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!

[arnesmits]

Great. Thank you for your efforts!

[mtmorgan]

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

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

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