Bioconductor/sweave2rmd: Conversion of howtogenefilter.Rnw to Rmd

[Khadeeejah]

@Bioconductor/sweave2rmd
My name is Khadijah an Outreachy applicant. I was assigned this issue on the project board,

@jwokaty Kindly review my PR.

HTML
PDF

[Khadeeejah]

@Bioconductor/sweave2rmd please review my contribution for Outreachy.
@jwokaty

[jwokaty]

Hi @Khadeeejah, Thanks for your pull request. We're going to use the following checklist for the review, doing a little bit at a time:

• the .Rmd file knits to HTML
• R CMD build runs without errors or timeouts
• the tarball from R CMD build contains the HTML (check with the
  following by substituting the package name and vignette name tar ztf package_name.tar.gz | grep 'doc/vignette_name')
• the .Rnw file has been removed
• in the DESCRIPTION, BiocStyle and knitr are listed in Suggests
• in the DESCRIPITON, the line VignetteBuilder: knitr exists
• any added lines use the same spacing and indents as the existing
  document
• if agreed with the Maintainer, the contributor is in the author list
  in the DESCRIPTION file; refer to the contribution guide for acceptable
  formats
• if agreed with the Maintainer, the contributor is in the author list
  in the vignette's YAML; refer to the contribution guide for acceptable formats
• if this pull request includes a conversion from using the separate Author
  and Maintainer lines into the Authors@R vector, check that the
  Authors@R vector includes the maintainer as specified with role='cre'.
• if this pull request includes a conversion from using the separate Author
  and Maintainer lines into the Authors@R vector, the Maintainer line
  is completely removed.
• HTML document is representative of the PDF in content and
  in general the presentation
• Where the contributor was not able to preserve the content and presentation
  of the PDF is noted as a comment in the pull request
• the R Markdown file is representative of the Sweave document and follows
  best practices, such as replacing links to Bioconductor packages with calls
  to BiocStyle's Biocpkg()

[jwokaty]

@Khadeeejah Please address these changes. I believe some of them, such as the inline code or blank spaces may appear again later in the document. Please also address those. Push your changes to this PR and let me know we're ready to continue the review.

[Khadeeejah]

@jwokaty thank you
I'll do everything right away ☺️

[Khadeeejah]

@jwokaty kindly review i have fixed all

[Khadeeejah]

@jwokaty i have updated my pull request
kindly check out my HTML FILE

[Khadeeejah]

@jwokaty

[jwokaty]

@Khadeeejah Can you please wrap long lines and check the correct syntax for code block names in the R Markdown cheatsheet?

[jwokaty]

@Khadeeejah Hi, I have marked additional issues, which are mostly minor, but these should be the final issues addressed before we can merge. Although I have mentioned it in another comment, please wrap all long lines and correct the naming of code blocks (there should be no comma between the r and the name of the code block.

[jwokaty]

@Khadeeejah Can I ask that you leave these unresolved? I will use them to recheck your code when you have pushed all your changes?

[Khadeeejah]

Good morning ma @jwokaty i have updated my PR.

[jwokaty]

Can you reformat lines 64-70 and 78-84?

[jwokaty]

Hi @Khadeeejah, I have 2 last changes to improve the formatting of 2 paragraphs. After you push the changes, provided that there are no new issues, I'll merge your PR.

[Khadeeejah]

@jwokaty i have formatted the two paragraphs, thank you

[jwokaty]

Thanks for your contribution! I'm merging your PR.

[Khadeeejah]

Thanks for your contribution! I'm merging your PR.

Thank you so much please can you assign the last vignette on the board to me or any other

I would love to contribute more