Closed cbiagii closed 4 years ago
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The DESCRIPTION file for this package is:
Package: pcitRif
Type: Package
Title: Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Version: 0.99.0
Authors@R: c(person("Carlos Alberto", "Oliveira de Biagi Junior", email = "cbiagijr@gmail.com", role = c("aut", "cre")),
person("Ricardo", "Perecin Nociti", email = "rnociti@gmail.com", role = c("aut", "ctb")),
person("Breno", "Osvaldo Funicheli", email = "osvaldobreno99@gmail.com ", role = c("aut", "ctb")),
person("João Paulo", "Bianchi Ximenez", email = "joaopaulo.ximenez@me.com", role = c("ctb")),
person("Patrícia", "de Cássia Ruy", email = "patiruy@gmail.com", role = c("ctb")),
person("Marcelo", "Gomes de Paula", email = "marcelogomesrp@gmail.com", role = c("ctb")),
person("Rafael", "dos Santos Bezerra", email = "rafaelbezerra50@yahoo.com", role = c("ctb")),
person("Wilson", "Araújo da Silva Junior", email = "wilsonjr@usp.br", role = c("aut", "ctb")))
Author: Carlos Alberto Oliveira de Biagi Jr [aut, cre], Ricardo Perecin Nociti [aut, ctb],
Breno Osvaldo Funicheli [aut, ctb], João Paulo Bianchi Ximenez [ctb],
Patrícia de Cássia Ruy [ctb], Marcelo Gomes de Paula [ctb],
Rafael dos Santos Bezerra [ctb], Wilson Araújo da Silva Junior [aut, ctb]
Description: This vignette provides the necessary instructions for performing the Partial
Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008)
and Regulatory Impact Factors (RIF) (Reverter et al. 2010) algorithm. The PCIT
algorithm identifies meaningful correlations to define edges in a weighted network
and can be applied to any correlation-based network including but not limited to
gene co-expression networks, while the RIF algorithm identify critical Transcription
Factors (TF) from gene expression data. These two algorithms when combined provide a
very relevant layer of information for gene expression studies (Microarray, RNA-seq
and single-cell RNA-seq data).
Imports: crayon, clusterProfiler, DESeq2, geomnet, GGally, ggplot2, ggpubr, graphics,
network, pbapply, reshape2, scales, stats, SummarizedExperiment, utils, dplyr, tidyr,
ggrepel
Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
Depends: R (>= 3.6), methods
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
biocViews: Sequencing, RNASeq, Microarray, GeneExpression, Transcription,
Normalization, DifferentialExpression, SingleCell, Network,
Regression, ChIPSeq, ImmunoOncology, Coverage
VignetteBuilder: knitr
Maintainer: Carlos Alberto Oliveira de Biagi Junior <cbiagijr@gmail.com>
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This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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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:
fbba190 Update DESCRIPTION
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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@LiNk-NY Hi Marcel!! It seems the package has passed the initial automated tests. I would very much like your feedback on the package so I can make the recommended changes and get this rolling. Thanks a lot for your time !
Hi Carlos, @cbiagii I have a couple of packages ahead of you in the queue. I will get to your package as soon as possible. Thank you.
Dear Marcel, don't worry! Thanks for the answer.
Hi Carlos, @cbiagii
Thank you for your submission. Please see the review below. If you have any questions, feel free to post them in the comments below.
Best, Marcel
Authors@R
section is overflowing. Please maintain it within 80 column
width.*input
, *input1
, and *input2
and related methods point out a potential
area of improvement for the package*Data
functions may not be necessary (see below)BiocManager::install("cbiagii/pcitRif")
cat
inside a function unless it is the show method. Use
message
insteadcountsToTPM
can have a funcitonal argument that guides the conversion with
the default being the original computation.anno = NULL
) so
the test is not relevant, use is.null
.df[, "sample1"]
instead of df[, 1]
.ifelse
. Use a table of data to reassign values, see
Martin Morgan's response in this stackoverflow link:
https://stackoverflow.com/questions/39217432/r-improving-nested-ifelse-statements-multiple-patternspcitrif
class. A list
of lists does not have much structure.SummarizedExperiment::assay
) for
PCITinput*
and related functions. This can also apply to the data accessor
functions raw/tmp/norm *Data
.@
accessor and create dedicated accessor functions for your
classtolerance
arguments a
,
b
, c
.Dear Marcel, @LiNk-NY , Thank you so much for your review on my package. I'm sure when I implement these recommended changes the package will look much better. I will start working on the modifications now, as soon as I have everything ready I will reply your comment with the revisions topic by topic.
Received a valid push; starting a build. Commits are:
f95b08c Bioconductor Review Fixes
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.
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.
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.
@mtmorgan, @lshep and @LiNk-NY , I changed the package name and consequently the repository name. Can you check so I can trigger a new build? Thanks!
Dear @LiNk-NY , Thank you very much for the review. I have made the solicited changes to ceTF package. If there is something else to fix, please let me know. Thanks!!
pcitRif #1329
- Consider renaming the package to something that is easier to remember. Packages with a lot of acronyms are not usually.
DESCRIPTION
- It looks good.
- The
Authors@R
section is overflowing. Please maintain it within 80 column width.
NAMESPACE
*input
,*input1
, and*input2
and related methods point out a potential area of improvement for the package*Data
functions may not be necessary (see below)
vignettes
- Please keep the text within the 80 column width margin. It makes the source document easier to maintain and to review.
- You do not need to explicitly install the dependencies for the package, a simple installation of the package will automatically get them for the user. Use
BiocManager::install("cbiagii/pcitRif")
R
- Avoid using
cat
inside a function unless it is the show method. Usemessage
instead
countsToTPM
can have a funcitonal argument that guides the conversion with the default being the original computation.
- Arguments with default values will not be missing (e.g.,
anno = NULL
) so the test is not relevant, useis.null
.
- Avoid using index positions to subset and rather opt for names when subsetting. For example, use
df[, "sample1"]
instead ofdf[, 1]
.
- Combine R files that are related to each other for example, some plotting functions can be in the same file.
- Avoid using nested
ifelse
. Use a table of data to reassign values, see Martin Morgan's response in this stackoverflow link: https://stackoverflow.com/questions/39217432/r-improving-nested-ifelse-statements-multiple-patterns
- Consider providing a more robust prototype for the
pcitrif
class. A list of lists does not have much structure.
- It seems like creating accessors for specific inputs is not the right way to go. Please create one general function that will access different parts of the object based on an argument (similar to
SummarizedExperiment::assay
) forPCITinput*
and related functions. This can also apply to the data accessor functions raw/tmp/norm*Data
.
- Usually, class names and package names match in case and class names have their first letters capitalized.
- Avoid using
@
accessor and create dedicated accessor functions for your class
- Please provide a more thorough description of the
tolerance
argumentsa
,b
,c
.
Hi Carlos, @cbiagii
You may also want to match the package case with the class case, i.e., CeTF
.
This is convention for many packages such as SummarizedExperiment
, SingleCellExperiment
, LoomExperiment
, etc.
Dear Marcel, @LiNk-NY I just updated the name of package to CeTF, as suggested. I updated too the repository name and added a new webhook to the repository. I need the confirmation of @mtmorgan to trigger a new version to make the automated build. Thanks!
Hey @cbiagii (cc @mtmorgan, @lshep, and @LiNk-NY),
I have changed the name of the package in our database so you should be good to kick off another build.
Best, Kayla
Received a valid push; starting a build. Commits are:
0abd588 Update DESCRIPTION
Thank you so much, @Kayla-Morrell!! Have a nice week. Best!!
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.
Received a valid push; starting a build. Commits are:
50e6fb6 Update DESCRIPTION
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.
Received a valid push; starting a build. Commits are:
7d508c7 Update DESCRIPTION
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.
Received a valid push; starting a build. Commits are:
f74ebe9 Update DESCRIPTION
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.
Dear Marcel, @LiNk-NY , I fixed a minor errors, and now it's all OK with the automated build!! Thanks.
Hi Carlos, @cbiagii Thanks for making those changes. Your package has been accepted. Thank you for your contribution!
Best, Marcel
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!
@LiNk-NY, Thank you for accepting the package. I am so glad to have worked with you these days and I am at your disposal for anything. Thanks very much,
Carlos Biagi Jr
The master branch of your GitHub repository has been added to Bioconductor's git repository.
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