appreci8R

[sandmanns]

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[bioc-issue-bot]

Hi @sandmanns

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: appreci8R
Type: Package
Title: appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV 
Version: 0.99.0
Author: Sarah Sandmann
Maintainer: Sarah Sandmann <sarah.sandmann@uni-muenster.de>
Description: The appreci8R is an R version of our appreci8-algorithm - A Pipeline for
    PREcise variant Calling Integrating 8 tools. Variant calling results of our 
    standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer,
    samtools and VarDict), as well as up to 5 additional tools is combined, evaluated
    and filtered.
License: LGPL-3
Encoding: UTF-8
LazyData: true
Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, VariantFiltering, SummarizedExperiment
Suggests: GO.db, org.Hs.eg.db
biocViews: VariantDetection, GeneticVariability, SNP, VariantAnnotation, Sequencing, 
RoxygenNote: 6.0.1

[bioc-issue-bot]

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[bioc-issue-bot]

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[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.

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

ae473ff updated mafByOverlap

[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, 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:

db4a8f3 remove system files

[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.

[bioc-issue-bot]

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

56bb87a simplify examples

[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.

[sandmanns]

The appreci8R imports quite some other R-packages. I think, this is why the installation takes a while and why the R CMD check exceeds the limit of 5 minutes in case of Windows (on Linux and OS X it seems to be faster). I already minimized the examples. And actually, I do not know what to do in addition to speed up the "check". Do you have any ideas on what I could do to speed it up? Or would you maybe review the appreci8R despite this remaining Warning...? :-) Thanks a lot in advance!

[lshep]

Since this check is clear on MAC and Linux I will review the package and ignore this WARNING. I will have a technical review in a few days.

[sandmanns]

Cool! Thank you so much! I am looking forward to it!

[lshep]

Hello, Very nice package. Please see the following comments:

Build Report

• [ ] Unit tests are good practice. Highly recommend adding a few
• [ ] Clean up coding practice note about 1:...

Data

• [ ] Please include a inst/script/ file that describes how the data in extdata was generated (can be sudo code or text). It should have some details on the instrumentation used and settings used for generation of files.
• [ ] Is there a reason existing data sets of bam files (like from Rsamtools) could not be used and you needed to include your own?

Vignette

• [ ] Please remove intermediate files (toc/tex/etc) - should only need the Rnw file as the vignette will be generated automatically.
• [ ] We are updating our installation methods. Please Update biocLite to BiocManager::install("appreci8R")

filterTarget function

• [ ] it seems like it should also be able to take in a GenomeRanges object for targetRegions
• [ ] Could this function be designed to work with a vcf object read in using VariantAnnotation::readvcf() as that is the standard Bioconductor way for importing a vcf file.
• [ ] A more standard output for this representation rather than a list is a GRangesList.

General Objects reporting genomic positioning should be converted to a GenomicRanges or GRangesList from the GenomicRanges package. This is a very common and consistent representation throughtout Bioconductor. This is true for all the input and output of your functions (rather than data.frames or lists of data.frames). The other option would be the VariantAnnotation representation for vcf like a CollapsedVCF

Please address or comment on the above issue. When ready please perform another version bump and comment back here for a re-review. Cheers Lori

[bioc-issue-bot]

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

efdf221 address reviewer comments

[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.

[sandmanns]

Dear Lori,

Thanks a lot for your very quick feedback! These are my comments on the points you mentioned:

Build Report

• [ ] Unit tests are good practice. Highly recommend adding a few -> Currently there are no unit tests. However, each functions contains internal checks to make sure files exist, input is not empty etc. so that the functions don't crash. Would that be okay?
• [x] Clean up coding practice note about 1:... -> The only cases of 1:... that remain are lines like: temp2<-cbind(temp1[,1:3],etc...) As temp1 is an internal object, I know that it contains (more than) 3 columns. Would it be okay to keep it like this?

Data

• [x] Please include a inst/script/ file that describes how the data in extdata was generated (can be sudo code or text). It should have some details on the instrumentation used and settings used for generation of files. -> included inst/script/information.txt; this is hopefully okay? file contains information on all files present in inst/extdata (how they were generated etc.)
• [ ] Is there a reason existing data sets of bam files (like from Rsamtools) could not be used and you needed to include your own? -> We hope that the appreci8R performs equally well on all data sets of bam files. However, for the exemplary data, we had the following idea: We developed the appreci8R on the basis of our appreci8 pipeline. In our paper, we present the analyses of a wide set of samples (training and test samples). We invested a lot of work into validating the numerous mutations, polymorphisms and artifacts detected in these samples. So, after all we are quite confident considering biological truth for these samples. For the exemplary data, we included two samples from the original training data set. The BAM files files (containing more than just 2 exemplary regions) are available via the NCBI SRA and information on all mutations and polymorphisms (and artifacts that were detected by various tools) in these samples are available as supplementary information. We liked to include these samples as exemplary data as we are confident about the categorization of their calls as mutations, polymorphisms and/or artifacts. So, we know that the appreci8R performs correctly on these sampels. And in case a user is interested to extend the example, he or she can download the complete BAM from the SRA.

Vignette

• [x] Please remove intermediate files (toc/tex/etc) - should only need the Rnw file as the vignette will be generated automatically.
• [x] We are updating our installation methods. Please Update biocLite to BiocManager::install("appreci8R")

filterTarget function

• [x] it seems like it should also be able to take in a GenomeRanges object for targetRegions
• [ ] Could this function be designed to work with a vcf object read in using VariantAnnotation::readvcf() as that is the standard Bioconductor way for importing a vcf file. -> We opted against this solution when writing the package for the following reasons: Although vcf files should be the standardized output format of any variant calling tool, we experienced that several tools (e.g. VarScan or Vardict) report (differently structured) txt files. Thus, it would always be the necessary to convert one to the other, as the txt-files cannot be read in as vcf files. Or - even easier - to read in vcf files (and txt files) as data.frames. That's what we decided to do. Additionally, CollapsedVCF objects need more storage compared to data.frames. If input from a very sensitive calling or WES results are analyzed, this aspect can be essential.
• [ ] A more standard output for this representation rather than a list is a GRangesList. -> We see your point that a GRangesList would be the more standard output. Unfortunately, it is a bit impractical to realize it for this function. The input of the different variant calling tools has not been normalized yet. As we just report chr and pos in our list of data.frames, coversion to chr, start and end has to be done via information on ref and alt. In the non-normalized form this is can be quite challenging (e.g. C > T,A or G > -C). To define a proper IRanges for the GRanges objects, normalization is inevitable. Well, it would be impractical to normalize everything twice, right? So, if possible, I would really like to keep the data.frame for this very first function.

General

• [x] Objects reporting genomic positioning should be converted to a GenomicRanges or GRangesList from the GenomicRanges package. This is a very common and consistent representation throughtout Bioconductor. This is true for all the input and output of your functions (rather than data.frames or lists of data.frames). The other option would be the VariantAnnotation representation for vcf like a CollapsedVCF -> Fixed for all functions except for filterTarget (see comment above)

The WARNING was again just on Windows, because it took 5 minutes and 8 seconds... :-)

Best, Sarah

[lshep]

Thank you for providing justification for the above implementation and thank you for converting to GenomicRanges for the majority of the output. The package looks good and I will allow the few exceptions to the build report.

[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!

[sandmanns]

Thank you so much for this great, quick review! Just let me know in case there is anything left I can do.

Looking forward to seeing the appreci8R on Bioconductor :-)

Best, Sarah

[mtmorgan]

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