IdentifiHR

[ashleyweir1]

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• Repository: https://github.com/DavidsonGroup/IdentifiHR

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[bioc-issue-bot]

Hi @ashleyweir1

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: IdentifiHR
Type: Package
Title: IdentifiHR: predicting homologous recombination (HR) status for high-grade serous ovarian caricnoma (HGSC) using gene expression
Version: 0.99.0
Author: @R: 
    c(person(given = "Ashley L", 
  family = "Weir",
  role = c("aut", "cre"),
  email = "weir.a@wehi.edu.au",
  comment = c(ORCID = "0000-0002-3072-2616")))
Description: IdentifiHR is a trained logistic regression model that can predict HR status, being HR deficient (HRD) or HR proficient (HRP), in addition to the probability of a sample being HRD, using only gene expression. IdentifiHR first subsets raw gene expression counts collected from RNA sequencing to only those required for count transcormation and scaling (n = 2604 genes), and then uses the weighted abundances of 209 of these genes to predict HR status in HGSC.
Depends: R (>= 3.5.0)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
Imports:
    dplyr,
    tibble,
    edgeR,
    glmnet,
    stats
RoxygenNote: 7.3.2
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: GeneExpression, RNASeq, Classification

[ashleyweir1]

I have updated the DESCRIPTION file and made necessary changes. The updated version is now available on GitHub with version 0.99.1. Please consider the new version for review. Thank you!

[lshep]

Please adapt to also use standard Bioconductor object for gene expression, SummarizedExperiment

[ashleyweir1]

Hi, I have updated my main branch so that the package can also use SummarizedExperiment objects. However, I want to double check - do I have access to the Bioconductor git server, to push these changes to the remote branch? Thank you for your help.

[lshep]

at this point you do not have git access yet. We will check your github branch shortly

[lshep]

In the description your license is gpl3 + file license but I only see the gpl3 license included in the package. I think you should remove the + file license as it does not seem needed

Could you also add a section in the vignette to show the use of the Bioconductor class. And update the man pages/documentation to indicate as such

[ashleyweir1]

Hi, Thank you for bringing these needed changes to my attention - I have updated the license listed in the DESCRIPTION and the vignette to document SummarizedExperiment objects as input, though I believe the man pages/documentation for the functions where this change is relevant have already been updated. Kindly, Ashley

[lshep]

Your vignette uses a data.frame of "rawCounts" not a SummarizedExperiment object? Did you not push to the github repo? Your man pages mention SummarizedExperiment but again use data.frame. Please add a SummarizedExperiment example in the vignette -- there are lots of available existing SummarizedExperiments in other packages or ExperimentHub if needed.

[ashleyweir1]

Hi, I apologise for the confusion. I have added examples specifically and pushed to the repo. Please let me know if anything else is needed - thank you for your help, Ashley