icetea

[vivekbhr]

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[bioc-issue-bot]

Hi @vivekbhr

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: icetea
Type: Package
Title: Integrating mRNA Cap Enrichment with Transcript Expression Analysis
Version: 0.99.0
Authors@R: person("Vivek", "Bhardwaj", email = "bhardwaj@ie-freiburg.mpg.de", role = c("aut", "cre"))
Description: icetea is a tool that integrates the cap enrichment information
    obtained from transcript 5' profiling methods like MAPCap and RAMPAGE,
    with the analysis of transcript expression. It provides functions for
    end-to-end analysis : from raw reads to detection of transcription
    start sites and performing differential TSS detection between group
    of samples.
Depends:
    R (>= 3.6)
Imports:
    stats,
    utils,
    methods,
    graphics,
    grDevices,
    ggplot2,
    GenomicFeatures,
    ShortRead,
    BiocParallel,
    Biostrings,
    S4Vectors,
    Rsamtools,
    BiocGenerics,
    IRanges,
    GenomicAlignments,
    GenomicRanges,
    rtracklayer,
    SummarizedExperiment,
    VariantAnnotation,
    limma,
    edgeR,
    csaw,
    TxDb.Dmelanogaster.UCSC.dm6.ensGene
Suggests:
    knitr,
    rmarkdown,
    Rsubread (>= 1.29.0),
    testthat
VignetteBuilder: knitr
biocViews: Transcription, GeneExpression, Sequencing,
    RNASeq, Transcriptomics, DifferentialExpression
URL: https://github.com/vivekbhr/icetea
BugReports: https://github.com/vivekbhr/icetea/issues
License: GPL-3 + file LICENSE
LazyData: true
RoxygenNote: 6.0.1

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[bioc-issue-bot]

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[vobencha]

Sorry for the delay on this. I'll get you a review tomorrow.
Valerie

[vobencha]

Hi,

I've done a first review. Please see comments / suggestions below and let me know if you have any questions.

1. package name

I don't see where you define what icetea stands for. While the letters may stand for 'integrating cap enrichment transcript expression analsyis' I doubt that will be immediately obvious to anyone. I would suggest putting this in 'Description' of DESCRIPTION and the vignette.

It's good you have several biocViews so at least it will be categorized and hopefully users will have an idea of what the package does.

2. Please remove LazyData = true. This has been shown to slow down library() calls, especially when the package has large data.

3. non-exported functions

You don't have to create man pages for functions that you do not export. If you do create them, they should be complete.

For example, ResizeReads is not exported but the man page has several problems:

\name{ResizeReads}
\alias{ResizeReads}
\title{preprocess reads to count only 5' overlaps}
\usage{
ResizeReads(reads, width = 1, fix = "start")
}
\arguments{
\item{reads}{GAlignment object}

\item{width}{New read length}

\item{fix}{'Start' for 5'}
}
\value{
Resized reads as GRanges
}
\description{
preprocess reads to count only 5' overlaps
}

• 'width' and 'fix' should be specified as character

• add an example

• the description is unclear since the function simply resizes the ranges

All this function does is call GenomicRanges::resize. Do you really need a separate function for this?

 ResizeReads <- function(reads, width = 1, fix = "start") {
     reads <- as(reads, "GRanges")
     stopifnot(all(GenomicRanges::strand(reads) != "*"))
     GenomicRanges::resize(reads, width = width, fix = fix)
 }  

Please revisit the non-exported functions and decide if they are worth keeping. If they are, add detail to the man pages.

4. newCapSet class

Why not re-use FastaFile or FastaFileList as input and SummarizedExperiment or as output? If you are set on creating your own S4 class it should extend RangedSummarizedExperiment.

5. imports / exports

A package in 'imports' in DESCRIPTION should be fully or selectively imported in NAMESPACE. For example, these packages are in 'imports' but not mentioned in NAMESPACE.

~/repos/github/packageReview/icetea >grep ShortRead NAMESPACE
~/repos/github/packageReview/icetea >grep BiocParallel NAMESPACE
~/repos/github/packageReview/icetea >grep Biocstrings NAMESPACE

This is not a comprehensive list. Please go through DESCRIPTION and check the packages against NAMESPACE.

6. R file names

I would recommend renaming the R files to match the function name and man page. For example, detect_TSS.R -> detectRSS.R.

~/repos/github/packageReview/icetea/R >ls
AllClasses.R         detect_diffTSS.R    get_geneCounts.R      splitBAM_byIndex.R
AllGenerics.R        detect_TSS.R        mapCaps.R             splitBAM_byRepindex.R
annotate_TSS.R       example_CSobject.R  methods.R             utils.R
demultiplex_fastq.R  filterDuplicates.R  plotting_functions.R

[vivekbhr]

Thanks for the review Valerie. I would try to fix them soon

[bioc-issue-bot]

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

3512d0d version bump
4f7e8c3 Merge pull request #33 from vivekbhr/develop vers...

[vivekbhr]

@vobencha Thanks for the review. Here are some changes I made so far :

package name

I modified the description to add what icetea stands for. (Integrating Cap Enrichment with Transcript Expression Analysis)

Please remove LazyData = true.

DONE

non-exported functions

I improved description of ResizeReads and other non-exported functions. I don't need the man pages but I would like to keep the roxygen style comments in the code so I end up generating them.

I want to keep the function ResizeReads since 1) I use this multiple times in the package. 2) we are thinking of using the package for iCLIP analysis in future, where the users would like to have the signal from the end or the middle of the reads.

newCapSet class

The purpose in my mind when creating the class was to use a container for all file paths (fastq and BAMs) along with mapping statistics, also to make it easy to check certain assumptions and fail early in the analysis.

I tried using RangedSummarizedExperiment, but I am not able to use any of its functionality. In principle, I could fit my sampleInfo DataFrame as colData and other information as metadata in the SE object. But the former throws an error (due to no assay column) and the latter requires me to skip the validity checks. Would appreciate any suggestions here.

imports / exports
I added atleast one import from each package into namespace (through roxygen directive @importfrom ), but I have still not listed all required functions there since that would mean removing all my package::function syntax from the code. I want to keep the package::function syntax in my code to : 1. avoid a function masking another 2. it's easier for me to come back after years and find which function came from which package. I could still add all imports for each of my functions through roxygen if this is absolutely required.

R file names

DONE

[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:

03cd512 trying to fix bioc build check
cbc0fae version bump
777aaa1 Merge pull request #34 from vivekbhr/develop tryi...

[bioc-issue-bot]

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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[vivekbhr]

My build is passing on all platforms through appveyor and travis . Can someone point out the issue here? (I already tried listing the .gitattributes file in .Rbuildignore)

[bioc-issue-bot]

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

551bb72 removing .gitattributes
8d1e6da Merge pull request #35 from vivekbhr/develop remo...

[bioc-issue-bot]

Dear Package contributor,

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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:

68579bf fixed issues with bioparallel
1dbef1a adding bpisup()
fbf2a8e adding Xvector version (concatenateobjects error o...
17f3867 typo
8af0354 updating travis .yaml to fix caching issue, also u...
321b9b3 travis agai
148c386 travis again
5bd7ebf Merge pull request #36 from vivekbhr/develop fixe...

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

8d084ac removing versions: :
bda3cb4 removed versions
ed012de Merge pull request #37 from vivekbhr/develop Deve...

[bioc-issue-bot]

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

43eda77 trying to downgrate S4vectors to fix build)
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75b7795 Merge pull request #38 from vivekbhr/develop Deve...

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

cb0586a remove deps
2a55535 Merge pull request #39 from vivekbhr/develop remo...

[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.

Please see the build report for more details.

[bioc-issue-bot]

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

4426e74 fix check for NA
a03c941 Merge pull request #40 from vivekbhr/develop fix ...

[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.

Please see the build report for more details.

[bioc-issue-bot]

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

e6df250 skip suggested packages in windows build
e0680db version bump
4ec51eb Merge pull request #41 from vivekbhr/develop Deve...

[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.

Please see the build report for more details.

[vivekbhr]

@vobencha I have fixed all issues with the build errors except the error with RSubread on windows. Please have a look at my replies above and let me know if additional changes are required.

Best,
Vivek

[vobencha]

Thanks for making the changes.

If you want to keep RSubread in Suggests you'll need to add a .BBSoptions file as described by Herve in
https://stat.ethz.ch/pipermail/bioc-devel/2018-May/013667.html
This file should go at the same level at R/ man/ etc.

Valerie

[vivekbhr]

@vobencha It's there already. It's just not being recognized by the build system at the moment.

[vobencha]

Yes, I know the SPB does not recognize this option and the error will persist until the package is built on the formal build system. I had missed the file in the github repo when I looked for it last time. Thanks for adding it.

[bioc-issue-bot]

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[mtmorgan]

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