(inactive) iCNV

[zhouzilu]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/zz327/iCNV

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[bioc-issue-bot]

Hi @zhouzilu

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: iCNV
Title: Integrated Copy Number Variation detection
Version: 0.0.2
Authors@R: c(person("Zilu", "Zhou", email = "zhouzilu@pennmedicine.upenn.edu", role = c("aut", "cre")),
                person('Nancy','Zhang', email='nzh@wharton.upenn.edu'), role = c("aut"))
Author: Zilu Zhou, Nancy Zhang
Maintainer: Zilu Zhou <zhouzilu@pennmedicine.upenn.edu>
Description: Integrative copy number variation (CNV) detection from multiple platform and experimental design.
Depends: R (>= 3.3.1)
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Imports:
  fields,
  ggplot2,
  truncnorm,
  tidyr,
  data.table,
  dplyr
Suggests: knitr,
    rmarkdown
VignetteBuilder: knitr
biocViews: ExomeSeq, WholeGenome, SNP, CopyNumberVariation, HiddenMarkovModel

[mtmorgan]

Before being added to our moderation and review queue, your package needs to be updated to (a) interoperate with existing Bioconductor sequence-related packages, e.g., GenomicRanges, Summarized Experiment and (b) have a 'real' vignette with evaluated code chunks, rather than a static vignette with 'pictures of code'.

Please update your package in this way, and post a short comment indicating that it is now ready to be reviewed to this issue, mentioning @mtmorgan .

[zhouzilu]

@mtmorgan Hi Martin, Thank you for the review. I actually had a few questions regarding to your comments.

• Where should I add the interoperate, in the Description?
• I was intending to build a 'real' vignette, but this package initialed from BAM files and vcf, which is too large to put in a package, and kind of hard to processing as well. Do you have any idea how to solve this?

Thanks

[mtmorgan]

These are not review comments, but rather 'pre-review', before a review is possible.

Usually interoperability involves adding Bioconductor packages to the Depends: or Imports: fields of the DESCRIPTION file, coupled with appropriate use of Bioconductor data structures particularly as argument or return values to the functions that your package defines. Use of Bioconductor structures inside a package is at the discretion of a package author.

Usually vignettes are based on realistic but trimmed-down data (e.g., part of a chromosome) that does fit into the package guidelines for space and size, or that re-uses an existing 'ExperimentData' package; it is sometimes appropriate to also submit a new ExperimentData package or ExperimentHub resource (there is a vignette in the ExperimentHub package describing how resources can be contributed).

[zhouzilu]

Thank you. I will modify my github site and will let you know.