TimeSeriesExperiment

[nlhuong]

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

• Repository: https://github.com/nlhuong/TimeSeriesExperiment

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.

[bioc-issue-bot]

Hi @nlhuong

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: vistimeseq
Type: Package
Title: Analysis for short time-course sequencing data
Version: 0.99.0
Date: 2018-09-30
Author: Lan Huong Nguyen
Maintainer: Lan Huong Nguyen <nlhuong90@gmail.com>
Description: Visualization and analysis toolbox for short time course data 
  which includes dimensionality reduction, clustering, two-sample differential 
  expression testing and gene ranking techniques. The package also provides 
  methods for retrieving enriched pathways.
License: LGPL (>= 3)
Depends:
  R (>= 3.5)
VignetteBuilder: knitr
Imports:
    Biobase,
    circlize,
    dynamicTreeCut,
    dplyr,
    edgeR,
    DESeq2,
    ggplot2,
    graphics,
    grDevices,
    grid,
    Hmisc,
    limma,
    methods,
    magrittr,
    proxy,
    RColorBrewer,
    stats,
    tibble,
    tidyr,
    vegan,
    viridis,
    utils
Suggests:
    knitr,
    GO.db,
    org.Mm.eg.db,
    org.Hs.eg.db,
    MASS,
    rmarkdown,
    ComplexHeatmap,
    UpSetR,
    testthat
Encoding: UTF-8
RoxygenNote: 6.1.0.9000
biocViews: TimeCourse, Sequencing, RNASeq, Microbiome,
    GeneExpression, Transcription, Normalization, DifferentialExpression,
    PrincipalComponent, Clustering, Visualization, Pathways
BugReports: https://github.com/nlhuong/vistimeseq/issues
URL: https://github.com/nlhuong/vistimeseqv

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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:

f4d035f bump up version for Bioconductor new build 21d9c94 add importfrom methods for function is() 447b4c3 fix documentation and bugs

[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:

9a81095 bump the version up

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[mtmorgan]

DESCRIPTION / etc

• ok

vignette

• consider using BiocFileCache to maintain a local cache of the GSE counts, to avoid excessive downloads during nightly builds
• typo 'ExressionSet' should be 'ExpressionSet'. See comments on SummarizedExperiment
• Is the GSE file in the vignettes directory used? If not, please remove.

R

• Generally looks good
• ExpressionSet functionality has largely been repleaced by SummarizedExperiment for sequence-based analysis.
• Is there a reason that you did not extend SummarizedExperiment instead of creating your own class from scratch? This is a more robust and interoperable solution.
• Generally, avoid exposing user to internals of object implementation, e.g., plots.R:38 '"feat_desc" not in feature_data(object)

tests

• looks like there are no tests; too bad! might as well remove the unused infrastructure

NEWS

• make sure NEWS can be parsed by utils::news()

[nlhuong]

Hi,

I am working currently on implementing your suggestions, and have the following questions so far.

1. SummarizedExperiment: I will add a functionality to convert between SummarizedExperiment and vistimeseq objects. However, I did not decide on building vistimeseq by extending the SummarizedExperiment class, due to differences in the focus. vistimeseq should be applicable to a wide variety of rectangular data where samples have a corresponding time. I did not want all the utilities offered by SummarizedExperiment to confuse the user.

• The main difference is that vistimeseq works around a single assay. These should not be any more assays allowed, as other slots are generated based on that single data table.

• In vistimseq, I designed the slots to center around time, and require a specific design (number of samples for each timepoint must be the same for each group and replicate). If this condition is not met, the counts are imputed. I found that generating a class from scratch helps to keep it simpler and allows for easier way to check validity and cross matching between different slots.

• Another reason is stylistic. I keep all my function names with a "_" separator syntax, ad did not want to include CamelBack notation of SummarizedExperiment functions which would be inconsistent with my package and confusing to the user.

Thus, I think re-writing the class as a SummarizedExperiment extensions would require a lot of work, with little advantage, and result in additional weaknesses of for the package.

2. BioFileCache seems to be buggy. I installed the package from the Bioconductor and call:

library(BiocFileCache)
url1 <- paste0("https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE114762&",
              "format=file&file=GSE114762_raw_counts.csv.gz")
cnts <- read_csv(bfcrpath(BiocFileCache(ask = FALSE), rnames = url1))

which which results in an error: Error in vapply(rnames, function(bfc, rname) { : values must be length 1, but FUN(X[[1]]) result is length 0

Do you have any recommendations as to how to resolve this?

Thanks!

[mtmorgan]

I do not insist that you use SummarizedExperiment, but feel that extending well-tested code i s likely to result in more robust and interoperable software than ad hoc class implementation. Stylistically, Bioconductor users expect CamelCase class names and camelCase function names.

I see the error you mention when using the release version of BiocFileCache, but not the devel version. Are you using the devel version of Bioconductor packages to test your code? This is where your package will be introduced to Bioconductor. I think your cache is corrupt (multiple resources with identical rname) and needs to be cleaned up

bcfquery(BiocFileCache(), rname=url1, exact = TRUE)  # several resources
bfcremove(BiocFileCache(), rids = paste0("BFC", 1:3))  # e.g.

For version I have

> sessionInfo()
R version 3.5.1 Patched (2018-10-05 r75405)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Users/ma38727/bin/R-3-5-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-3-5-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocFileCache_1.5.7 dbplyr_1.2.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19     digest_0.6.18    crayon_1.3.4     dplyr_0.7.7
 [5] assertthat_0.2.0 rappdirs_0.3.1   R6_2.3.0         DBI_1.0.0
 [9] magrittr_1.5     RSQLite_2.1.1    httr_1.3.1       pillar_1.3.0
[13] rlang_0.2.2      blob_1.1.1       bindrcpp_0.2.2   tools_3.5.1
[17] bit64_0.9-7      glue_1.3.0       bit_1.1-14       purrr_0.2.5
[21] compiler_3.5.1   pkgconfig_2.0.2  memoise_1.1.0    bindr_0.1.1
[25] tidyselect_0.2.5 tibble_1.4.2

[bioc-issue-bot]

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

b4654ea bump up version and edit travis

[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, 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:

05df5df bump version

[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, 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.

[nlhuong]

It seems that the BiocFileCache fails for Windows but not other platforms.

Also, do you have any recommendations for speeding up the check part? My package exceeds the limit time my around 1 second.

[mtmorgan]

thank you for the changes, I will review them today. The Windows problem will be addressed through a fix to BiocFileCache; do not worry about the Mac timing.

[mtmorgan]

vignettes

• It might be easier to write the urls as a vector

  urls <- paste0(
      "https://www.ncbi.nlm.nih.gov/geo/download/",
      "?acc=GSE114762&format=file&file=",
      c(
          "GSE114762_raw_counts.csv.gz", "GSE114762_gene_data.csv.gz",
          "GSE114762_sample_info.csv.gz"
      )
  )

• The use of BiocFileCache() can be simpified; you're using the default cache, so it does not need to be mentioned in the call

  library(BiocFileCache)
  
  cnts <- read_csv(bfcrpath(rnames = urls[1])) %>%
    column_to_rownames("X1") %>%
    as.matrix()
  ...

• A typo 'ExressionSet' is still present

NEWS

• Compare the output of your NEWS and the NEWS of a package like Rsamtools

  utils::news(Version == "1.33", package="Rsamtools")
  utils::news(Version == "0.99.0", package="vistimeseq")

[bioc-issue-bot]

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

5245540 fix typos and NEWS

[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.

[nlhuong]

Hi,

I have thought about your comments about extending SummarizedExperiment class and decided to change my package.

I have pushed my changes to vistimeseq/extendSE branch but now I would like to name my package TimeSeriesExperiment which I think is more in line with the Bioconductor conventions.

I have a few WARNINGS I do not know how to resolve to the new package based on extending SummarizedExperiment class:

❯ checking for missing documentation entries ... WARNING
  Undocumented S4 methods:
    generic 'assays' and siglist 'TimeSeriesExperiment'
    generic 'colData' and siglist 'TimeSeriesExperiment'
    generic 'colnames<-' and siglist 'TimeSeriesExperiment'
    generic 'rowData' and siglist 'TimeSeriesExperiment'
    generic 'rownames<-' and siglist 'TimeSeriesExperiment'
  All user-level objects in a package (including S4 classes and methods)
  should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking Rd \usage sections ... WARNING
  Undocumented arguments in documentation object 'assays'
    ‘withDimnames’
  Objects in \usage without \alias in documentation object 'assays':
    ‘\S4method{assays}{TimeSeriesExperiment}’

  Objects in \usage without \alias in documentation object 'colData':
    ‘\S4method{colData}{TimeSeriesExperiment}’

  Objects in \usage without \alias in documentation object 'colnames':
    ‘\S4method{colnames<-}{TimeSeriesExperiment}’
    ‘\S4method{rownames<-}{TimeSeriesExperiment}’

  Undocumented arguments in documentation object 'rowData'
    ‘use.names’
  Objects in \usage without \alias in documentation object 'rowData':
    ‘\S4method{rowData}{TimeSeriesExperiment}’

  Functions with \usage entries need to have the appropriate \alias
  entries, and all their arguments documented.
  The \usage entries must correspond to syntactically valid R code.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking dependencies in R code ... NOTE
  Unexported object imported by a ':::' call: ‘S4Vectors:::selectSome’
    See the note in ?`:::` about the use of this operator.

1. Could you advise me on how to get rid of these warnings?
2. How should I update the changes to the package for this issue (including the change of the package name)? What should I keep increasing the version number > 0.99.5 or reset?
3. Will we be able to make changes before the deadline for Bioconductor 3.8?

Thank you, Lan

[mtmorgan]

Since your class 'contains' SummarizedExperiment, it is not necessary to define methods assay() etc; the existing methods just 'work'. You still want to import the generic or importMethods the methods.

Obviously your user would like to work with your objects using the SummarizedExperiment interface; it makes sense to put SummarizedExperiment in the Depends: field. If instead you leave as an import, and then re-export specific methods, then yes it is necessary to re-document these, probably on a page that says 'see the SummarizedExperiment documentation'. But this seems like extra work and confusing to your user; it is better to put SummarizedExperiment in Depends:

The "objects in \usage without \alias" come from documentation where the \usage{} section references a method that is not in the \alias{} section, for instance man/assay.Rd has

\S4method{assays}{TimeSeriesExperiment}(x, ..., withDimnames = TRUE)

and so needs

\usage{assays,TimeSeriesExperiment-method}

Currently \usage{assays} says that you're going to document the generic, but actually you don't and this should be removed.

Both of these issues seem to come from the use of the roxygen tag @name; remove it and the documentation looks better. I don't know if this is a bug or somehow 'feature'. I think also you can add a specific @aliases assays,TimeSeriesExperiment-method.

Continue to make version bumps. Rename the repository to TimeSeriesExperiment. Update (edit the comment) the url in the first comment on this issue to point to the correct repository. Let me know when you are ready, and we'll adjust things on our end; you'll then have to do a version bump to trigger a new package build.

[mtmorgan]

We will try to get the package into the 3.8 release; the sooner the changes are complete the more likely we are for success...

[nlhuong]

Thank you for your help!

I have changed the dependencies and now TimeSeriesExperiment depends on SummarizedExperiment. As I understand, I do not have to document the methods. I do need to re-write a few setter methods though, so that they affect new slots of my class. I still get the warnings about the generics. Even with the examples like the following:

#' @importMethodsFrom SummarizedExperiment "rowData<-"
#' @export
setReplaceMethod("rowData", "TimeSeriesExperiment", function(x, ..., value) {
    if(nrow(value) != nrow(x))
        stop("nrow(value) does not match the input object dimensions.")
    if(!"feature" %in% base::colnames(value)) {
        stop("rowData data must contain columns 'feature'.")
    }
    if(!all(value$feature == rownames(x))) {
      rownames(x) <- value$feature
    }
    newobject <- callNextMethod()
    validObject(newobject)
    return(newobject)
})

#' @importFrom methods slot slot<-
#' @export
setReplaceMethod(
  "colnames", "TimeSeriesExperiment", function(x, value) {
    if(length(value) != ncol(x))
      stop("Wrong length of substitute vector for colnames.")
    newobject <- x
    colnames(newobject) <- value
    # Additionally modify the dimensionRediuction slot
    dimreds <- slot(newobject, "dimensionReduction")
    if(is.null(names(dimreds))) return(newobject)
    for (name_mat in names(dimreds)[grep("_sample", names(dimreds))]) {
        base::rownames(dimreds[[name_mat]]) <- value
    }
    slot(newobject, "dimensionReduction") <- dimreds
    validObject(newobject)
    return(newobject)
  }
)

How do I import the generics from SummarizedExperiment so that the warning goes away?

Thank you!

[mtmorgan]

Can you be specific about the warnings that you get? If you define a method, then you DO need to document the new method; if there are no methods defined but existing methods are useful to the user, they do NOT need to be documented by you.

[bioc-issue-bot]

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

1a239e6 changing the class to summarizedexperiment extensi... 6cd44f0 changing the class to summarizedexperiment extensi... 0604ac6 Change vistimeseq class to TimeSeriesExperiment, a...

[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.

[nlhuong]

Hi @lshep , I am changing the name for the package and have renamed the repository and edited the comment for this issue. Should I now edit the issue title? Could you sync the issue? Thanks, Lan

[lshep]

I have updated the issue in our database. Yes please change the issue title and you should be all set. Let us know if you run into any issues.

[nlhuong]

Thank you!

[bioc-issue-bot]

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

85affcd fix class methods

[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:

7a97022 fix documentation

[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:

35193c2 fix documentation for windows

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[nlhuong]

Hi, the package now has no warnings and errors. Please let me know if you can review it, as it seems today is the deadline for commits for 3.8 version.

[bioc-issue-bot]

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

d554092 update NEWS 49b1fce bump version

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[nlhuong]

Hi @mtmorgan!

My package passes the build and checks and is ready for re-review. Please see if it is ready to be accepted.

Thank you! Lan

[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]

Thanks for your work on this; I think the package has been improved!

[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/nlhuong.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(\"TimeSeriesExperiment\"). The package 'landing page' will be created at

https://bioconductor.org/packages/TimeSeriesExperiment

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.