(inactive) corrmeta

[wsjung]

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

• Repository: https://github.com/wsjung/corrmeta

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[bioc-issue-bot]

Hi @wsjung

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: corrmeta
Title: Correlated Meta-Analysis (corrmeta)
Version: 0.99.0
Author: Woo Seok Jung <jungw@wustl.edu>,
        Michael Province <mprovince@wustl.edu>
Maintainer: Woo Seok Jung <jungw@wustl.edu>
Authors@R: c(
    person("Woo Seok","Jung", role = c("aut","cre"), email = "jungw@wustl.edu"),
    person("Michael","Province", role = c("aut"), email = "mprovince@wustl.edu")
  )
Description: Performs Correlated Meta-Analysis (corrmeta) across multiple OMIC
        scans, accounting for hidden non-independencies between elements of the
        scans due to overlapping samples, related samples, or other information.
biocViews: Genetics, GenomeWideAssociation, SNP, StatisticalMethod, Software
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr
LazyData: true
Suggests:
    testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, qpdf
Config/testthat/edition: 3
Imports: 
    dplyr,
    polycor,
    stats,
    tidyr,
    magrittr

[lshep]

This package currently lacks any integration with any Bioconductor infrastructure class for OMICS data. Could you please expand the vignette and examples to show how this integrates into a workflow using Bioconductor class structures. Please also expand to compare to existing Bioconductor packages that do similar functionality to state improvements and/or differences.

[wsjung]

This package is not limited to any particular OMIC as its purpose is to perform meta analysis using p-values accounting for correlations based on the distribution of said p-values. I don't see where Bioconductor class structures would play a role in this package. Could you point me to a specific guideline in the developer docs that requires the use of Bioconductor base classes? I can't pinpoint anything in the contributing guidelines documentation.

[vjcitn]

have a look at MungeSumstats for example gwas representation that you could use for meaningful interop

[lshep]

The link you listed is also out of date; we will correct this. Package guidelines can be found at http://contributions.bioconductor.org in particular http://contributions.bioconductor.org/important-bioconductor-package-development-features.html

[lshep]

may we expect updates to address the above concerns?

[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.

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