Closed richardheery closed 8 months ago
Hi @richardheery
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: methodical
Title: Discovering genomic regions where methylation is strongly associated with transcriptional activity
Version: 0.99.0
Authors@R:
person("Richard", "Heery", , "richardheery@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-8067-3114"))
Description: DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of
potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples.
Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly
associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework,
lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and
transcriptional activity at transcriptional start sites.
License: GPL (>= 3)
BugReports: https://support.bioconductor.org/tag/methodical
biocViews: DNAMethylation, Transcription, MethylationArray, Software
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.2
Depends:
GenomicRanges,
ggplot2,
R (>= 2.10),
SummarizedExperiment
LazyData: false
Imports:
Biostrings,
BSgenome,
cowplot,
data.table,
DelayedArray,
doParallel,
dplyr,
foreach,
GenomeInfoDb,
HDF5Array,
IRanges,
RcppRoll,
rhdf5,
rtracklayer,
S4Vectors,
scales,
tibble,
tidyr
Suggests:
AnnotationHub,
BSgenome.Athaliana.TAIR.TAIR9,
BSgenome.Hsapiens.UCSC.hg38,
knitr,
methrix,
rmarkdown
VignetteBuilder: knitr
It looks like you are using kallisto in some functionality but it is not listed as a system dependency. See http://contributions.bioconductor.org/description.html#description-sysdep
If files are downloaded from external sources (like illumina, gencode, etc) we highly recommend using caching mechanism to help users with subsequent runs and to be able to use offline. See BiocFileCache.
I've added kallisto as a system dependency in the description and also an INSTALL file stating where it can be downloaded from. The only call to download a file is in an example which isn't run (for the kallisto_index function). Would it still be better to cache this file?
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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Hi Dario,
I'm just in the process of adding another vignette, which should be finished over the next day or two.
Cheers,
Richard
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Hello,
The only issue I seem to be having is a timeout due to some of the examples taking a while to run. Could we still add it to the manifest and I'll find some faster examples?
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@lshep I haven't received any feedback yet, but I'm passing all checks now. I just have one warning as I call library inside some of my code. I think this is justified since I do this while setting up a cluster wrapping the call in suppressMessages as I don't want to print the package startup messages on each node to the user.
The methodical package provides a set of analyses for DNA methylation data. It largely does not conform to the development guidlines set out in the Package Developer's Guide which is the second check box of the initial checklist above.
=
operator. See Code Syntax section of R Code chapter.Variables and function names use snake_case
style. See Function Names and Variable Names sections.
Using consistent variable and function naming style helps users when switching between Bioconductor packages.
mcrpc_wgbs_hg38_chr11 = download_meth_dataset(dataset = "mcrpc_wgbs_hg38_chr11")
download.file("https://zenodo.org/record/8422703/files/mcrpc_transcript_counts.tsv.gz"
Please refer to Chapter 13 Package Data's Other Data section.
Downloads of files and external data from the web should be avoided.
transcript_annotation = rtracklayer::import.gff3("gencode.v38.annotation.gff3.gz")
This should be obtained via AnnotationHub.
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", eval = FALSE)
Please change eval
to TRUE
and resubmit the package.
library(DESeq2)
but it is not in Suggests. Please read Chapter 6: The DESCRIPTION File for what to put in your DESCRIPTION file. There is also an indirect dependency on R.utils.> download.file("https://zenodo.org/record/8422703/files/mcrpc_transcript_counts.tsv.gz", destfile = "mcrpc_transcript_counts.tsv.gz")
trying URL 'https://zenodo.org/record/8422703/files/mcrpc_transcript_counts.tsv.gz'
Content type 'application/octet-stream' length 13824482 bytes (13.2 MB)
downloaded 13.2 MB
> mcrpc_transcript_counts = data.frame(data.table::fread("mcrpc_transcript_counts.tsv.gz"), row.names = 1)
Error in data.table::fread("mcrpc_transcript_counts.tsv.gz") :
To read gz and bz2 files directly, fread() requires 'R.utils' package which cannot be found. Please install 'R.utils' using 'install.packages('R.utils')'.
There is no checking of input variable type. S4 methods should be considered because they have a signature
which does this. Alternatively, use !is(parameter, Class)
.
Parallelisation uses doParallel
package. Bioconductor packages must use BiocParallel framework. See Package Reiewer Checklist.
Some functions seem to reimplement what already exists in Bioconductor and is maintained by the core team. For example, expand_granges
is essentially
genomic_regions_starts[on_plus] = genomic_regions_starts[on_plus] - upstream
genomic_regions_starts[on_minus] = genomic_regions_starts[on_minus] - downstream
genomic_regions_ends[on_plus] = genomic_regions_ends[on_plus] + downstream
genomic_regions_ends[on_minus] = genomic_regions_ends[on_minus] + upstream
which is already available in GenomicRanges as the promoters
or perhaps flank
function.
Major revisions required.
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Thanks for your feedback @DarioS .
I think I have addressed most of your comments now:
. I changed the output of vignettes to BiocStyle::html_document and added chunks for installing the package . I replaced = with <- for variable assignment. . I now use camelCase for function names. I left internal variables used by functions in snake_case as I found the code became difficult to read otherwise. . The WGBS and RNA-seq count datasets are now donwloaded from the TumourMethData ExperimentHub package. . I am now using AnnotationHub to retrieve the transcript annotation used by the vignette. . I changed the vignette options so that all code is evaluated. . I added dependencies for DESeq2 and R.utils . For each function, I now check the class of each input variable using is(). . Parallelization now makes use of BiocParallel . I removed the expand_granges() function since GenomicRanges::promoters() can be used to achieve the same thing.
I still have some warnings regarding the use of suppressWarnings(), but I think this should be retained as otherwise thousands of warnings can be printed to the user's screen.
Let me know if there is anything else you think should be addressed.
%dopar%
.> head(tubb6_cpg_meth_transcript_cors)
data frame with 0 columns and 0 rows
>
> # Extract the location of the TSS from the results
> attributes(tubb6_cpg_meth_transcript_cors)$tss_range
NULL
@richardheery did you see the above comment on re-review and may we expect changes soon?
Hi, sorry I was very busy with the submission of a paper, but I should be able to address the comments and resubmit within the next week or so.
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