oncomix

[dpique]

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

• Repository: https://github.com/dpique/oncomix

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[bioc-issue-bot]

Hi @dpique

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: oncomix
Title: Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA
    Expression Data
Version: 0.99.0
Author: Daniel Pique, John Greally, Jessica Mar
Maintainer: Daniel Pique <daniel.pique@med.einstein.yu.edu>
Description: This package helps identify mRNAs that are overexpressed in subsets
    of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal
    data from the same tissue from many patients (>15 pairs). This unsupervised
    approach relies on the observation that oncogenes are characteristically
    overexpressed in only a subset of tumors in the population, and may help
    identify oncogene candidates purely based on differences in mRNA expression
    between previously unknown subtypes.
Depends:
    R (>= 3.4.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests:
    knitr,
    rmarkdown,
    testthat,
    RMySQL
Imports:
    ggplot2,
    ggrepel,
    RColorBrewer,
    mclust,
    stats
VignetteBuilder: knitr
biocViews: GeneExpression, Sequencing

[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: "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 following build report for more details:

http://bioconductor.org/spb_reports/oncomix_buildreport_20170918173031.html

[bioc-issue-bot]

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

8303868 subscribed to bioc-devel list

[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/oncomix_buildreport_20170918184246.html

[nturaga]

oncomix Review

R CMD build: ok

R CMD INSTALL: ok

DESCRIPTION

• Ok

• No bioconductor packages being used.

  NAMESPACE

• ok

  vignettes

• ok. Good job.

  man

• ok

  R

• Wouldn't it be easier if dfNml, and dfTumor were just matrices? Support the class SummarizedExperiment as input to your function.

• Accept transposed data, where rows are genes and patients are columns, which is common in bioinformatics.

• Replace 1:ncol (L:58:oncoMix_two_component_mixture_models.R) to seq_len(ncol(dfNml))

  data

• Describe the data more, i.e how they were obtained and processed.

[bioc-issue-bot]

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

1affef8 added 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.

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/oncomix_buildreport_20171010191802.html

[dpique]

Hi @nturaga,

Thanks for your feedback on my package. I have listed the changes as sub-bullet points below each of your comments.

Please let me know if there's anything that needs clarification.

Best, Daniel

DESCRIPTION

• No bioconductor packages being used.
  • I added compatibility with the SummarizedExperiment class (see below) to improve integration of oncomix with Bioconductor and standard container classes.

R

• Wouldn't it be easier if dfNml, and dfTumor were just matrices? Support the class SummarizedExperiment as input to your function.
  • Yes. I added a new function, toMatrix, to convert SummarizedExperiment and data.frame objects to matrices. I added toMatrix to the body of functions where dfNml and dfTumor – which are now matrices – are used as inputs.
  • I renamed dfNml and dfTumor to exprNml and exprTum to avoid confusion about the object class that is required as input (now that several matrix-like classes, not just a dataframe (df), can be used as input to the mixModelParams and plotGeneHist functions).
• Accept transposed data, where rows are genes and patients are columns, which is common in bioinformatics.
  • I rearranged the functions to accept matrices in which the rows are genes and patients are columns.
• Replace 1:ncol (L:58:oncoMix_two_component_mixture_models.R) to seq_len(ncol(dfNml))
  • I made this change, and I also updated the man examples to include seq_len() where possible.
• Other:
  • I updated the description of the return value for the mixModelParams function.

data

• Describe the data more, i.e how they were obtained and processed.
  • I added descriptions on how the data were obtained and processed to the man pages. I also changed the dataset names (dfNmlIsof and dfTumorIsof are now exprNmlIsof and exprTumIsof, respectively) because these objects are now matrices and not dataframes (df).

[nturaga]

Hi @dpique

Once you are ready with the changes, please provide a brief summary for each point. I will review your package again after you reply.

[dpique]

Hi @nturaga,

Thanks for your message. I updated the package based on your feedback, and a summary of the changes that I made are listed below. Please let me know if there's anything that needs clarification. Looking forward to hearing your feedback on this new set of changes.

Best, Daniel

DESCRIPTION

• I added compatibility with the SummarizedExperiment class (see below) to improve integration of oncomix with Bioconductor.

R

• I added a new function, toMatrix, to convert SummarizedExperiment and data.frame objects to matrices. I added toMatrix to the body of functions where dfNml and dfTumor – which are now matrices – are used as inputs.

• I renamed dfNml and dfTumor to exprNml and exprTum to avoid confusion about the object class that is required as input (now that several matrix-like classes, not just a dataframe (df), can be used as input to the mixModelParams and plotGeneHist functions).

• I rearranged the functions to accept matrices in which the rows are genes and patients are columns.

• I replaced 1:ncol (L:58:oncoMix_two_component_mixture_models.R) with seq_len(ncol(dfNml)). I also updated the man examples to include seq_len() where possible.

• I updated the description of the return value for the mixModelParams function.

data

• I added descriptions on how the data were obtained and processed to the man pages. I also changed the dataset names (dfNmlIsof and dfTumorIsof are now exprNmlIsof and exprTumIsof, respectively) because these objects are now matrices and not dataframes (df).

[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.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/dpique.keys is not empty), then no further steps are required. Otherwise, do the following:

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2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

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(\"oncomix\"). The package 'landing page' will be created at

https://bioconductor.org/packages/oncomix

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.