SCOPE

[rujinwang]

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• Repository: https://github.com/rujinwang/SCOPE

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[bioc-issue-bot]

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

9991136 revision

[rujinwang]

Hi @hpages , Thanks a lot for your comments and constructive suggestions. I have been working on this paper revision and it took a bit longer. I've made changes accordingly and bumped the package to a new version. To be specific, Previously discussed

You've saved them as GRanges objects. Why couldn't you pass a GRanges object to a function?

Yes, thanks for your suggestion! The current version does not load pre-stored dataset in the global environment.

Those are the chromosome lengths of hg38 (see seqinfo(getBSgenome("hg38"))), not hg19.

Yes, you are correct. I loaded the bam files into IGV and confirmed it's hg38. I made changes in function examples by specifying their reference genome to be hg38.

So if you have a range of 1 million bases where only the 1st position overlaps with a bin of mappability 0.5 and the 999999 other positions overlap with a bin of mappability 1, and the two bins have the same size, you're considering that the mappability of your range is 0.75? Even though 99.9999% of the range has a mappability of 1? How does that make sense?

Regarding mappability calculation, I agreed with you that the one below would make more sense. get_mapp() has been adjusted.

• (mapp_A x size_overlap_with_A + mapp_B x size_overlap_with_B) / (size_overlap_with_A+size_overlap_with_B)

Other things

• Argument default values with NULL have been reset. get_bam_bed(), get_mapp() and get_gc have been updated.
• The exclamation marks at the end of your error messages have been removed.

Please feel free to let me know if further improvements are needed. Thank you for your kind help!

Best regards, Rujin

[bioc-issue-bot]

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

5cb8516 minor edit

[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.

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[bioc-issue-bot]

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

b504522 fix timeout

[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.

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[bioc-issue-bot]

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

bcec208 0.99.10

[bioc-issue-bot]

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

021820f get_gc() dontrun

[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". 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.

[rujinwang]

Hi @hpages , Just want to check in on it. I have been working on improving the package. Feel free to let me know your comments. Thank you.

Best, Rujin

[hpages]

Thanks for letting me know. Will take a look ASAP.

[bioc-issue-bot]

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

7a8c494 add algorithms with shared clonal memberships

[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". 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.

[hpages]

Thanks @rujinwang. Package is good to go.

[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!

[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/rujinwang.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

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

https://bioconductor.org/packages/SCOPE

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.

[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/rujinwang.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("WGSmapp"). The package 'landing page' will be created at

https://bioconductor.org/packages/WGSmapp

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.