Closed SimoneTiberi closed 5 years ago
Hi @SimoneTiberi
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The DESCRIPTION file for this package is:
Package: BANDITS
Type: Package
Title: BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Version: 0.99.0
Date: 2019-02-19
Author: Simone Tiberi
Maintainer: Simone Tiberi <simone.tiberi@uzh.ch>
Description: BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts,
via differential transcript usage (DTU),
between two or more conditions.
The method uses a Bayesian hierarchical framework, which allows for sample specific proportions
in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts.
Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed
via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.
biocViews: DifferentialSplicing, AlternativeSplicing, Bayesian, Genetics,
RNASeq, Sequencing, DifferentialExpression, GeneExpression, MultipleComparison,
Software, WorkflowStep, Transcription
License: GPL (>= 3)
Depends: R (>= 3.6.0)
Imports: Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, methods, stats, graphics, ggplot2,
DRIMSeq, BiocParallel
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr,
tximport, BiocStyle
SystemRequirements: C++11
ByteCompile: false
VignetteBuilder: knitr
RoxygenNote: 6.1.1
URL: https://github.com/SimoneTiberi/BANDITS
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Hi @Kayla-Morrell I think the package is ready for review when you have time.
Have a good one, Simone
Hello @SimoneTiberi,
Perfect! I'll comment back here in a week or so with my initial review.
Best, Kayla
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Hello @SimoneTiberi,
Thank you for submitting to Bioconductor. Please see the initial review of your package below. Comment back here with updates that have been made and when the package is ready for a re-review. Please keep in mind the deadline to accept packages into this release cycle is 4/24, therefore changes should be made in timely manner so as to give enough time for a re-review and any additional changes.
[ ] SUGGESTION: no visible binding for global variables
[ ] SUGGESTION: Consider clarifying how 5 objects are initialized
[ ] SUGGESTION: For formating reasons consider shorter lines, 992 lines are > 80 characters long.
[ ] SUGGESTION: For formating reasons Consider multiples of 4 spaces for line indents, 1948 lines are not.
See FormatR package (https://cran.r-project.org/web/packages/formatR/index.html) for formating help.
[ ] REQUIRED: 'LazyData' should be 'FALSE'. If set to 'TRUE' it can slow down the loading of packages with data.
[ ] REQUIRED: 'GenomicFeatures' and 'Biostrings' should be listed under 'Suggests' since they are used in the vignette.
[ ] SUGGESTION: We strongly encourage including a 'BugReports:' tag that points to a relevant Github for reporting issues. I would either add that tag with the url provided in 'URL' or just change the 'URL' tag to 'BugReports'.
\software{}
code is not redenering correctly.[ ] CLARIFICATION: Should the second author listed on the vignette be included as an author in the DESCRIPTION file?
[ ] SUGGESTION: We strongly suggest an 'Introduction' section for vignettes, so I would change the heading 'Abstract' to 'Introduction'.
[ ] REQUIRED: An 'Installation' section should be included (could come from your README file) that shows users how to download and load the package from Bioconductor.
[ ] REQUIRED: Line 106, the txt file is quoted incorrectly. The first two marks are `` and the last two marks are \'\'. Please change them to either \' \' or \" \".
[ ] REQUIRED: Line 164, 'length' is misspelled.
[ ] REQUIRED: Line 245, 'technically' is misspelled.
[ ] REQUIRED: Line 262, the help(BANDITS\_test)
does not work. Please provide the correct code.
[ ] REQUIRED: As an overall note for all of the man pages, edit the examples so that you are only showcasing the specific function in that man page. For example, in the man page BANDITS_data-class the usage of the function is show(object)
but I don't know where in the example this is demonstrated. Keep the examples simple, just enough information to show the user how they can use the function. Also, be sure code is not commented out in examples.
[ ] REQUIRED: The data man pages must include source information and data structure information. See http://r-pkgs.had.co.nz/data.html#data-data for help with this.
BANDITS-package
BANDITS_test-class
eff_len_compute
head(eff_len)
so the user can see a bit of how the output should look.filter_genes
[ ] REQUIRED: Avoid using direct slot access with '@', accessor methods should be created and utilized instead.
[ ] REQUIRED: Avoid for
loops, instead vectorize.
[ ] SUGGESTION: We prefer to see <-
instead of =
for assignment. Not a crucial change, just our syntax preference.
Best, Kayla
Hi @Kayla-Morrell, thanks for the feedback: I'll take care of it and re-submit the package.
A question/clarification: "REQUIRED: Avoid for loops, instead vectorize." I will try to minimize the presence of for loops, but a few are cumbersome to vectorize, I hope you will be fine with a couple of them being present.
We'll get back to you with the updated package in a few days.
Have a good one, Simone
@SimoneTiberi, a couple is not bad to have just as few as possible will help optimize the timing/speed of the functions.
I look forward to seeing the updated package.
Best, Kayla
Ok @Kayla-Morrell, thanks for the feedback.
Maybe I exaggerated with just a couple, but I noticed that most of the computationally intensive code is in Rcpp or already vectorized. Most of the remaining for loops are either necessary or would not benefit (computationally) from a vectorization: 1) in some loops the i-th iteration depends on the previous one; 2) in others, we modify only parts of existing objects; 3) in others we intialize several objects and, if vectorizing, I would still need a loop to allocate the resulting objects.
Btw, I implemented all 'REQUIRED' (still working to reduce some for loops) and some 'SUGGESTION': I will re-submit very soon.
Have a good one, Simone
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