epihet

[xiaowenchenjax]

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

• Repository: https://github.com/TheJacksonLaboratory/epihet

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

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[Liubuntu]

Hi @xiaowenchenjax ,

Yes it is possible to change the name of the package while under review.

1. Change your github repository first.
2. Update the github link (in first comment of this issue)
3. Update the issue name on the review.

After that, We will need to also make the change on our database of new issues. When the issue is renamed please ask @lshep on the issue number to rename the issue before making any additional version bumps to the package.

Best, Qian

[xiaowenchenjax]

Hi @Liubuntu, I see, it is too complex, it is easier to keep "epihet" this name. Thank you very much. Best, Xiaowen

[lshep]

It really is no trouble on our end to change the database if you wish to pursue the name change - entirely up to you.

[Liubuntu]

Hi @xiaowenchenjax ,

The steps only include updating the package name for 1) your own github repository, 2) the link to your updated github repository in the first comment of this issue and 3) this issue name.

If you want to keep the current name of "epihet", you will need to make the names consistent in your DESCRIPTION "Package" field, so that the current building error could be removed. A second review will be give only when you get a clean and successful building report. Thanks!

Best, Qian

[xiaowenchenjax]

Hi @Liubuntu , OK, thanks. i will update my package as soon as possible. Best, Xiaowen

[bioc-issue-bot]

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

b812098 checked DESCRIPYION, R/data.R 4fefa96 checked R/.R 10X, NAMESPACE 6c49d13 rerun roxygen c4f3d49 change package name from EpiHet to epihet 634dfae rename R functions 8cb05a8 revised all R/.R, rerun roxygenize(), check succe... aea929b add r sessioninfo to epihet.Rnw 1948d42 add install section in epihet.Rnw. Build, Check su... 0f0059e revised epihet.Rnw, build/check succeeded. Change ... 3d768fd Merge branch 'master' into dev_branch

[xiaowenchenjax]

Hi @Liubuntu , I update my package. i think this time should be OK. thanks

[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: "skipped, ERROR, 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 build report for more details.

[xiaowenchenjax]

Hi @Liubuntu , I check the warnings and error in the build report. for BiocCheck, WARNING: Update R version dependency from 3.5.1 to 3.6. In MACS, ERROR: dependency ReactomePA is not available for package epihet. Could you give me some suggestion how to fix it? Thank you very much Best, Xiaowen

[Liubuntu]

Hi @xiaowenchenjax ,

You can ignore the MAC dependency error for now. Please do for BiocCheck, WARNING: Update R version dependency from 3.5.1 to 3.6. as suggested, so that I could give another look at your updates. Thanks!

Best, qian

[xiaowenchenjax]

Hi @Liubuntu, OK. i will update R version dependency from 3.5.1 to 3.6. Do I need to update package version from 0.99.5 to 0.99.6? Thanks. Best, Xiaowen

[Liubuntu]

Yes. You need to bump version whenever you make any changes/updates so that it could trigger the building.

[xiaowenchenjax]

Hi @Liubuntu , Thanks. Best. Xiaowen

[bioc-issue-bot]

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

1c661f7 Update DESCRIPTION

[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: "skipped, TIMEOUT, 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.

[Liubuntu]

Hi @xiaowenchenjax ,

Please see below for the 2nd review. Please address the issues or comment back to explain why they are not addressed. Let me know for any question. Thanks!

R

Also check other scripts for similar issue. e.g., "diffHet(subtype, ...)", "epiBox(type, ...)", "epiMa(pval.matrix, )", "epiMap(annotate,)", "epiPCA(type, )", "epiTSNE(type, )", "modulevisual(value.matrix, )", "summarize(gr1, gr2, )", "userobj(data)", ...

The above argument checks, I mean the specific information that are required for the argument. E.g., in epiMA.R, check the column names / column contents would make more sense than checking the data class is(pval.matrix, "data.frame"). Same as the other functions above.

@param pval.matrix The data frame returned from the
#' diffHet() function that contains means, p-values,
#' adjusted p-values, and heterogeneity difference
#'

The following issues about coding style / best practices were from initial review and was not addressed with no explaination. These are strongly encouraged by Bioconductor, If making the modifications are too hard or causing unexpected delay in time with coordinating or anything else, please explain here.

• Do not need to test twice for logical values (diffHet.R:L58): if (length(loci.filter)>0) could be only: if (length(loci.filter)). Also in "epinetwork.R":L167.

• Avoid using of 1:..., use seq_len() or seq_along() instead.

• Please use " <- " for assignment instead of "=".

man/

Since all data are documented inside one "data.md" file, so in "R/data.R", there is no need for the duplicated @return A data frame. One would be enough.

Also for @format and @description, add a label before hand each description line with the data name, so the merged "data.md" file is more organized and easy to read. e.g.,

...
#' @description A data frame containing 31995 elements as background
used for pathway enrichment analysis:
#' @format background: A data frame with 31995 rows and 1 variables: ...
#' @return
#' A data frame
"background"

#' datTraits
#'
#' @description datTraits: clinical traits containing OS,EFS,age
#' @format datTraits: A data frame with 6 rows and 3 variables: ...
#' @return A data frame
      ## COMMENT: remove this section from "datTrait" and all duplicate sections from the documentation of other datasets. One "@return A data frame" from "background" would be enough.
"datTraits"

[xiaowenchenjax]

Hi @Liubuntu , I will look at it. Thanks. Xiaowen

[xiaowenchenjax]

Hi @Liubuntu, In my data.R file, It looks like this:

' Example data

' @docType data

' @keywords datasets

' @name background

' @rdname data

' @usage data(background)

' background

' @description background: A data frame containing 31995 elements as background used for pathway

' enrichment analysis

' @format background: A data frame with 31995 rows and 1 variables:

' \describe{

' \item{gene}{background gene list}

' }

' @return

' A data frame

"background"

' datTraits

' @docType data

' @keywords datasets

' @name datTraits

' @rdname data

' @usage data(datTraits)

' datTraits

' @description datTraits: Clinical traits containing OS,EFS,age

' @format datTraits: A data frame with 6 rows and 3 variables:

' \describe{

' \item{OS}{overall survival time}

' \item{EFS}{survival time}

' \item{age}{ages of patients}

' }

"datTraits" *But in the data.Rd file, i can only see the format and describe information for data frame "background" . Could you tell me how to fix it? \docType{data} \name{background} \alias{background} \alias{datTraits} \alias{DEG} \alias{DEH} \alias{diffhetmatrix} \alias{moduledm} \alias{modulesil} \alias{promoter} \alias{sharedmatrix} \title{background} \format{background: A data frame with 31995 rows and 1 variables: \describe{ \item{gene}{background gene list} }} \usage{ data(background) ......

[bioc-issue-bot]

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

dc4f7ef modify data.R 7d0ae1f compMatrix.R '=' to '<-' 8c57f51 modify compMatrix, DiffHet, epiBox, epiMap. revers... 032a5c4 modifyMA, check OK. modify epiNetwork, epiPathwayn... 6180b28 modify epiMA epiNetwork epiPathway epiPCA epiTSNE ... 6ac77a0 modify moduleSim moduleVisual readGR shannon split... 2cfaf94 revised according to bioconductor review

[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, skipped, TIMEOUT, 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.

[bioc-issue-bot]

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

a48385f Update DESCRIPTION

[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: "skipped, 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.

[Liubuntu]

Hi @xiaowenchenjax ,

Thanks for making updates. However, for coding styles, I would recommend you to check out here and here for any further development. It's highly recommended to use <- for R variable assignment instead of =, all through the code.

I'm accepting the package now. Thanks for your contribution to Bioconductor.

Cheers, Qian

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[xiaowenchenjax]

Hi @Liubuntu, Thank you! I learn from you a lot. i will check the link you send me and keep this coding style for further development. Best, Xiaowen

[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/xiaowenchenjax.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
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 BiocManager::install("epihet"). The package 'landing page' will be created at

https://bioconductor.org/packages/epihet

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.