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EDIRquery
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- Repository: https://github.com/lauravongoc/EDIRquery
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Hi @lauravongoc
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: EDIRquery
Title: Query the EDIR Database For Specific Gene
Version: 0.99.0
Authors@R:
person("Laura D.T.", "Vo Ngoc", , "[email protected]",
role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1597-900X"))
Description: EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.
License: GPL (>= 3)
Encoding: UTF-8
biocViews: Genetics, SequenceMatching
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Depends:
R (>= 4.1.0)
Imports:
tibble (>= 3.1.6),
tictoc (>= 1.0.1),
utils (>= 4.1.3),
stats (>= 4.1.3),
readr (>= 2.1.2)
Suggests:
knitr,
rmarkdown
VignetteBuilder: knitr
Thanks for this submission. The package does not use any Bioconductor data structures. A GRanges instance would probably be useful for
head(results)
#> chromosome repeat_length repeat_seq start end repeat_seq2 start2
#> 3930 17 7 CCGCGGG 80101595 80101602 CCGCGGG 80101734
#> 3931 17 7 CCGAGGC 80105602 80105609 CCGAGGA 80105843
#> 3932 17 7 CGGAGGG 80110005 80110012 GCGAGGG 80110061
#> 3933 17 7 CCAAGGG 80118254 80118261 CCGAGGG 80118270
#> 3934 17 7 CCGAGGG 80118270 80118277 GCGAGGG 80118318
#> 3935 17 7 CCGAGGG 80118270 80118277 CAGAGGG 80118533
#> end2 distance ensembl_gene_id hgnc_symbol gene_range
#> 3930 80101741 132 ENSG00000171298 GAA 80101556-80119881
#> 3931 80105850 234 ENSG00000171298 GAA 80101556-80119881
#> 3932 80110068 49 ENSG00000171298 GAA 80101556-80119881
#> 3933 80118277 9 ENSG00000171298 GAA 80101556-80119881
#> 3934 80118325 41 ENSG00000171298 GAA 80101556-80119881
#> 3935 80118540 256 ENSG00000171298 GAA 80101556-80119881
#> ensembl_transcript_id transcript_range intron_exon intron_exon2
#> 3930 ENST00000302262 80101581-80101890 E1 E1
#> 3931 ENST00000302262 80105133-80105748 I2 E3
#> 3932 ENST00000302262 80109945-80110055 E9 I9
#> 3933 ENST00000302262 80118193-80118357 E18 E18
#> 3934 ENST00000302262 80118193-80118357 E18 E18
#> 3935 ENST00000302262 80118193-80118357 E18 I18
#> feature mismatch
#> 3930 same exon 0
#> 3931 spanning intron-exon 1
#> 3932 spanning intron-exon 1
#> 3933 same exon 1
#> 3934 same exon 1
Please consider.
Thank you for your comment.
GRanges is not adapted for our data, as it only highlights a single range of positions, whereas each row in our data includes 2 sequences with their respective start and end positions, the distance between the two, as well as additional annotation.
How about the GenomicInteractions class? How about using DNAString to represent your sequences? Do you use Bioconductor with your data?
Hi, do you plan to work on interoperation of this package with Bioconductor? Please let us know.
Hi, apologies for the delay.
The package files in the repo have been updated with the added implementation of GInteractions class.
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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. 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
[email protected]:packages/EDIRquery to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: e952da1ddb5afa92aa47000e19691b020392f2ec
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 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
[email protected]:packages/EDIRquery to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @lauravongoc
I hope to look at this week, thank you for removing the warnings.
Best wishes, Olly
HI @lauravongoc
My apologies for the delay - it's be a busy month. Please see the following review before we can accept the package:
- [x] Bioconductor install instruction in the .readme and vignette
- [x] What does
sysdata.rdain the R folder do? I imagine this needs to be remove or moved - [x] package version should match between Descriptions and News
- [x] R to version >= 4.2
- [x] FIx a license, variable lincenses are not allowed
- [x] Do you need to import all of the packages and package functions in the NAMESPACE - export and import selectively if possible
- [x] Please add unit tests
- [ ] Avoid use of
catin R functions
Otherwise looks good - thank you!
Received a valid push on git.bioconductor.org; starting a build for commit id: fddb518e85ed44397557232632463b0a0be49e9f
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, skipped". 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
[email protected]:packages/EDIRquery to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5808626e484667e201eeb8028b6217456f4e0757
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, skipped". 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
[email protected]:packages/EDIRquery to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: fe27a2f3faf71de0acba79b458d04250036e924e
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 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
[email protected]:packages/EDIRquery to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @ococrook
Thank you so much for the review, and my apologies as well for the delay.
The above points have been addressed. Concerning the 2nd point, the file sysdata.rda in the R directory contains internal data that is parsed by the gene_lookup() function if no path parameter with additional data is not specified.
Great, thank you! Does the sysdata.rda have to be in the R folder, could it be moved to the data or inst folders?
Dear @ococrook,
Putting internal data in sysdata.rda in the R folder was done following the R Packages guidelines I referenced from Hadley Wickham & Jenny Bryan, specifically the Data section. I cannot seem to find a way to direct the calls to this data in the function to another source folder.
Yes I think this is okay as long as the sysdata.rda is documented and proper indication of source/licensing referenced (if not in a man page than in a file in inst/scripts)
Hi @lauravongoc
Sorry, it looks like I got confused which data was being referred where. As suggested, could you make it clear in the package what the data is and where it came from? If I understand correctly the documentation currently there is for the data in the /data folder?
Received a valid push on git.bioconductor.org; starting a build for commit id: 28c411219af96bba6eeed8036029b8e2e4ba7d2e
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 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
[email protected]:packages/EDIRquery to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @ococrook
Indeed the documentation that was already there was for the data in /data. I have now added documentation for the sysdata.R in the /inst/scripts/ folder as suggested.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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