Closed SimonSchlumbohm closed 1 year ago
Hi @SimonSchlumbohm
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: HarmonizR
Title: Handles missing values and makes more data available
Version: 0.99.0
Authors@R:
c(person(given = "Simon",
family = "Schlumbohm",
role = c("aut", "cre"),
email = "schlumbohm@hsu-hh.de"),
person(given = "Julia",
family = "Neumann",
role = "aut"),
person(given = "Philipp",
family = "Neumann",
role = "aut"))
Description: An implementation, which takes input data and makes it available
for proper batch effect removal by ComBat or Limma. The implementation appropriately
handles missing values by dissecting the input matrix into smaller matrices
with sufficient data to feed the ComBat or limma algorithm. The adjusted
data is returned to the user as a rebuild matrix. The implementation is
meant to make as much data available as possible with minimal data loss.
Depends: R (>= 4.2.0)
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: BatchEffect
Imports:
doParallel (>= 1.0.16),
foreach (>= 1.5.1),
janitor (>= 2.1.0),
plyr (>= 1.8.6),
sva (>= 3.36.0),
seriation (>= 1.3.5),
limma (>= 3.46.0)
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Interesting package. Have you considered the use of SummarizedExperiment or its derivates, or MultiAssayExperiment, for managing the combinations of phenotypes and assays that you are working with? This is a standard approach to dealing with multiple assays on multiple samples and we strongly encourage this approach.
Dear @vjcitn ,
thank you for your comment on the submitted package. We included support for the S4 SummarizedExperiment data type within the HarmonizR package and updated documentation accordingly. HarmonizR will now parse and return S4 SummarizedExperiment data to support more fluent data pipelining.
A version-bump to 0.99.1 has been made according to Bioconductor guidelines.
With best regards
Simon Schlumbohm
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Hi @SimonSchlumbohm
I'm very sorry for the delay. I've been out of office for July. The package looks really good and it very clear to follow. Some trivial things before acceptance:
=
so it is A = B
rather than A=B
. The former is much easier to read.Best wishes, Olly
Dear @ococrook
thank you for the response. The package has been modified in the following ways:
Sincerely
Simon Schlumbohm
Brilliant, thank you Simon
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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@vjcitn @ococrook @lshep I would like to express a thank you from my side to everyone who has been involved in the process.
Sincerely
Simon Schlumbohm
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