tiagochst commented 4 years ago

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

Repository: https://github.com/TransBioInfoLab/MethReg

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 4 years ago

Hi @tiagochst

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: MethReg
Type: Package
Title: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Version: 0.1.0
Authors@R: c(
    person("Tiago", "Silva", email = "tiagochst@gmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0003-1343-6850")),
    person("Lily", "Wang", email = "lily.wang@gmail.com", role = c("aut"))
      )
Maintainer: Tiago Chedraoui Silva <tiagochst@gmail.com>
Description: MethReg evaluates, annotates and prioritizes DNA methylation regions 
  (or sites) with high regulatory potential, which work synergistically with transcription
  factors to regulate target gene expressions, without any additional ChIP-seq data.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports:
    dplyr,
    plyr,
    GenomicRanges,
    SummarizedExperiment,
    DelayedArray,
    ggplot2,
    ggpubr,
    tibble,
    tidyr,
    S4Vectors,
    sesameData,
    stringr,
    readr,
    knitr,
    methods,
    stats,
    Matrix,
    MASS,
    rlang,
    pscl,
    IRanges,
    sfsmisc,
    progress
Suggests: 
    rmarkdown,
    testthat (>= 2.1.0),
    parallel,
    downloader,
    R.utils,
    dbplyr,
    RSQLite,
    DBI,
    doParallel,
    reshape2,
    prettydoc,
    JASPAR2020,
    TFBSTools,
    motifmatchr,
    matrixStats,
    biomaRt,
    dorothea,
    viper
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Depends: 
    R (>= 4.0)
biocViews:
  MethylationArray,
  Regression,
  GeneExpression,
  Epigenetics,
  GeneTarget,
  Transcription

tiagochst commented 4 years ago

I fixed the version from 0.1.0 to 0.99.0.

mtmorgan commented 4 years ago

The package needs to be available on the 'master' branch. Please ensure that BiocCheck::BiocCheck() passes without error or warning. Please post a comment here when your package satisfies these basic requirements.

tiagochst commented 4 years ago

Hi Martin,

I fixed it.

Here is the BiocCheck::BiocCheck().

tiagochst commented 4 years ago

@mtmorgan Please, do I need to do something else ?

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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LiNk-NY commented 4 years ago

Hi Tiago, @tiagochst

Thank you for your submission to Bioconductor. Please see the review below.

Best, Marcel

MethReg #1613

DESCRIPTION

Add more details to the Description: field.
Add a BugReports: link for issue reporting.

NAMESPACE

If possible, shorten function names.
You may want to import the entirety of GenomicRanges e.g., import(GenomicRanges) rather than using importFrom.

vignettes

Remove the GitHub installation instructions.
Show how to use BiocManager to install the package.
Remove the repeated library(MethReg) call in the vignette.
Avoid awkward constructions such as get(data(...)) in a user-facing vignette. data should return the data instead of a character. Perhaps use usethis::use_data.
Observe the 80 character width limit. It makes text easier to read and even maintain.
You don't need to remove the data object from memory with gc().
Remove any code for coMethDMR as it is not in Bioconductor or CRAN.

R

It is possible for the user to save a file themselves without the need of the file.out argument in your function. It may be more simple to remove the argument and include an example in the documentation that shows the user how to write the data to disk.
Avoid using dontrun{} in examples. This creates stale code whenever there is an API change.
If the dontrun examples are too computationally intense, I would suggest using a smaller example dataset.
The min.confidence argument does not match the documentation in R/create_triplet_regulon_based.R
Use caching such as BiocFileCache to avoid re-download of human_tfs resources.
Update documentation for dnam and others to include SummarizedExperiment as an option.
Avoid downloading files from an Amazon bucket. It is recommended that you obtain it from the official source or from ExperimentHub so that other users/developers can make use of the data (cRegulome.db.gz in R/get_tf_targets_cistrome.R).
I think the documented data in R/MethReg.R should be named rather than NULL. See usethis::use_data.

Minor:

Reduce repetitive code by combining logical tests, for example, if (missing(exp) || is.null(exp)) in R/cor_region_dnam_target_gene.R.
Allow users to turn off the verbosity from message function calls in functions like get_promoter_avg.

tests

Remove or update any commented code.
Looks good.

README.Rmd

Update installation instructions to use BiocManager instead of GitHub.

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bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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.

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bioc-issue-bot commented 4 years ago

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tiagochst commented 4 years ago

@LiNk-NY I made the updates requested.

I decided to remove get_tf_targets_cistrome.R since I was using it mainly for analysis in the article and it is not a requirement for the package. I had the function unexported, but I think removing makes more sense.

Those dontrun examples were taking some time to run due to the access of DNA methylation metadata information from the sesame package and there was a 20 min computation time limit from Bioconductor. I reviewed some of the examples and removed some dontrun examples.

For the function names here are some changes:

filter_genes_by_quantile_mean_fold_change -> filter_exp_by_quant_mean_FC
filter_regions_by_quantile_difference -> filter_dnam_by_quant_diff
make_se_from_dnam_probes ->make_dnam_se
make_se_from_gene_matrix -> make_exp_se

The other requirements were fixed.

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

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.

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LiNk-NY commented 4 years ago

Hi Tiago, @tiagochst

Thanks for making those changes. Can you please respond to the review line by line?

Best, Marcel

bioc-issue-bot commented 4 years ago

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tiagochst commented 4 years ago

@LiNk-NY Thanks for the extensive review! Below are the answers to each point.

DESCRIPTION

Add more details to the Description: field.

The description was modified from:

MethReg evaluates, annotated, and prioritizes DNA methylation regions (or sites) with high regulatory potential, which work synergistically with transcription factors to regulate target gene expressions, without any additional ChIP-seq data.

To:

Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.

https://github.com/TransBioInfoLab/MethReg/commit/49ac86d14caecb28041ea0e9b8fd68b6c454bd17#diff-35ba4a2677442e210c23a00a5601aba3

Add a BugReports: link for issue reporting.

BugReports was added: https://github.com/TransBioInfoLab/MethReg/issues/

NAMESPACE

If possible, shorten function names.

For the function names here are some changes:

filter_genes_by_quantile_mean_fold_change -> filter_exp_by_quant_mean_FC
filter_regions_by_quantile_difference -> filter_dnam_by_quant_diff
make_se_from_dnam_probes ->make_dnam_se
make_se_from_gene_matrix -> make_exp_se

You may want to import the entirety of GenomicRanges e.g., import(GenomicRanges) rather than using importFrom.

I imported GenomicRanges, but there was a warning of masked functions because I was importing dplyr. So I importedFrom dplyr instead of importing all its functions. However, importedFrom GenomicRanges was a easier solution, since dplyr functions were extensively used in the package.

vignettes

Remove the GitHub installation instructions.

Removed.

Show how to use BiocManager to install the package.

MethReg is a Bioconductor package and can be installed through BiocManager::install().

if (!"BiocManager" %in% rownames(installed.packages()))
     install.packages("BiocManager")
BiocManager::install("MethReg", dependencies = TRUE)

Remove the repeated library(MethReg) call in the vignette.

Removed.

Avoid awkward constructions such as get(data(...)) in a user-facing vignette. data should return the data instead of a character. Perhaps use usethis::use_data.

I normally use get(data(...)) when I need the object with another name instead of the default. But in this case it was not necessary.

object <- get(data(...)) was changed to data(...) only.

Observe the 80 character width limit. It makes text easier to read and even maintain.

I reduced as much as a could the width of the lines.

You don't need to remove the data object from memory with gc().

Removed.

Remove any code for coMethDMR as it is not in Bioconductor or CRAN. R

All the coMethDMR code was removed.

It is possible for the user to save a file themselves without the need of the file.out argument in your function. It may be more simple to remove the argument and include an example in the documentation that shows the user how to write the data to disk.

This option was removed https://github.com/TransBioInfoLab/MethReg/blob/master/R/cor_region_dnam_target_gene.R#L51-L58

Avoid using dontrun{} in examples. This creates stale code whenever there is an API change. If the dontrun examples are too computationally intense, I would suggest using a smaller example dataset.

Don't run examples were removed for the majority of the functions.

The min.confidence argument does not match the documentation in R/create_triplet_regulon_based.R

Thanks for catching this problem. Now the documentations have the same argument description: https://github.com/TransBioInfoLab/MethReg/blob/master/R/create_triplet_regulon_based.R#L12-L15 https://github.com/TransBioInfoLab/MethReg/blob/master/R/regulons.R#L32-L34

Use caching such as BiocFileCache to avoid re-download of human_tfs resources.

BiocFileCache was used for caching: https://github.com/TransBioInfoLab/MethReg/blob/master/R/get_human_tfs.R#L26-L44

Update documentation for dnam and others to include SummarizedExperiment as an option.

Thanks for noticing this problem. I added SummarizedExperiment as an option of input for the DNA methylation and gene expression input.

Avoid downloading files from an Amazon bucket. It is recommended that you obtain it from the official source or from ExperimentHub so that other users/developers can make use of the data (cRegulome.db.gz in R/get_tf_targets_cistrome.R).

This function was removed. https://github.com/TransBioInfoLab/MethReg/commit/a21dc6e5693dc7732de1d98f8c620afd8f1882a2

I think the documented data in R/MethReg.R should be named rather than NULL. See usethis::use_data.

All datasets were named rathen than NULL. https://github.com/TransBioInfoLab/MethReg/blob/master/R/MethReg.R

Minor: Reduce repetitive code by combining logical tests, for example, if (missing(exp) || is.null(exp)) in R/cor_region_dnam_target_gene.R.

Thanks for the suggestion. I changed it in some of the functions.

Allow users to turn off the verbosity from message function calls in functions like get_promoter_avg.

I added the verbose argument to the following functions: cor_tf_target_gene, get_promoter_avg,interaction_model, make_dnam_se, make_exp_se

This will silence the messages output from the function.

tests

Remove or update any commented code.

Commented code was removed

Looks good.

Thanks!

README.Rmd

Update installation instructions to use BiocManager instead of GitHub.

The installation instructions were updated to:

You can install the MethReg from Bioconductor with: BiocManager::install("MethReg")

bioc-issue-bot commented 4 years ago

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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/MethReg to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cb18c3254628b9ba32809c4a493f23fcf21edfdb

bioc-issue-bot commented 4 years ago

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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.

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LiNk-NY commented 4 years ago

Thanks for the detailed response. I've had a look at the changes and they look good! Thank you for contributing to Bioconductor. Best regards, Marcel

bioc-issue-bot commented 4 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

mtmorgan commented 3 years ago

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

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Bioconductor / Contributions

MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription #1613

MethReg #1613

DESCRIPTION

NAMESPACE

vignettes

R

tests

README.Rmd

DESCRIPTION

NAMESPACE

vignettes

tests

README.Rmd