bioc-issue-bot
commented
2 years ago Hi @mooredf22
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: protlocassign
Title: Compute constrained proportional assignments for
fractionated protein abundance
Version: 0.99.0
Date: 2022-02-26
Authors@R:
person(given = "Peter",
family = "Lobel",
role = c("aut"),
email = "lobel@cabm.rutgers.edu")
person(given = "Dirk",
family = "Moore",
role = c("cre","aut"),
email = "dirkfmoore@gmail.com")
Description: This package fits a constrained proportional assignment (cpa)
model to mass spectrometry data
to proportionally assign proteins to subcellular locations.
The package includes transformations to
improve the accuracy of the assignments as well as
facilities for simulating mixtures and evaluating
the perfomance of cpa on those mixtures.
Also included are facilities for summarizing spectral-level
data using random effects models to calculate average protein profiles.
License: GPL-3
Encoding: UTF-8
LazyData: false
Depends:
R (>= 4.1.0),
lme4
RoxygenNote: 7.1.2
Imports:
BB,
pracma,
outliers,
knitr,
stats,
graphics,
viridisLite,
viridis,
plot.matrix,
grid,
gridExtra,
rmarkdown,
utils,
methods,
BiocParallel
biocViews: Proteomics, MassSpectrometry
VignetteBuilder: knitr
URL: http//github.com/mooredf22/protlocassign
Suggests:
testthat (>= 3.0.0)
Config/testthat/edition: 3
vjcitn
mooredf22
lshep
lgatto
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
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[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
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[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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Comments: The "protlocassign" package presents R functions that take use mass spectrometry data from serial fractionation experiments to proportionally assign proteins to possibly multiple residences in subcellular organelles. The package includes seven vignettes that describe the methods in detail. There is also an accompanying manuscript describing the methods; a revision is under review.
Here are my comments on BiocCheck notes:
1 "Consider adding these automatically suggested biocViews: RNASeq"
This is not relevant to this proteomics-related package
2 "Recommended function length <= 50 lines."
Many of the functions that are longer than 50 lines create complex plots. There is no natural way to break them up into smaller components.
3 "Consider adding runnable examples to the following man pages which document exported objects:"
Most of the functions that are not service functions include runnable examples. The small number that are not are explained and illustrated in detail in the accompanying vignettes; setting up runnable examples for these functions withing the help files would be cumbersome.
4 "Consider shorter lines; 235 lines (3%) are > 80 characters long."
All lines in the functions are shorter than 80 characters. Much of the explanatory text in the vignettes are longer than 80 characters, and we believe that that text is readable and clear in its current form.
5 "Consider multiples of 4 spaces for line indents, 1133 lines(15%) are not."
We have chosen to use descriptive variable names in our code in order to clearly link them to the to the concepts explained in the vignettes and in the accompanying manuscript. As a consequence, some of these variable names are rather long, which makes it difficult to adhere strictly to the "multiples of 4 spaces" suggestion. We have chosen indentation amounts to be as readable as possible and also conform to the limit of 80 characters per line.
6 "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials).\nSubscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel" I am listed as the maintainer and I have subscribed to this mailing list.