adding css method

[SHillman836]

No description provided.

[antagomir]

Seems good. Just minor comments

[TuomasBorman]

Couple points from .calc_css_percentile function (I think that I fixed most of them already). The functions looked fine and it worked well, but there was room for improvement

1. Some of the indentations were incorrect. Should be multiplication of 4 spaces
2. Some lines were too long. Should be max 80 characters
3. Avoid loops. Vectorize if possible (faster than loops, and also good practice)
4. Instead of sapply, use vapply. (Comes from Bioconductor recommendations)
5. Instead of 1:10, use seq_len(10). (Comes also from Bioc)

[antagomir]

@Daenarys8 could you add the suggested updates and make a PR against the SHillman836::adding-css-method branch? Or can @SHillman836 help to finalize this one?

[TuomasBorman]

It seems that metagenomeSeq is only used in testing? We can probably just hard-code those values to testing file. That way we do not need this new dependency.

[Daenarys8]

we can ask them?

Sure. I found an existing issue from March this year and updated it. It seems the package had been inactive for a while.

[codecov]

Codecov Report

Attention: Patch coverage is 83.09859% with 12 lines in your changes missing coverage. Please review.

Please upload report for BASE (devel@3f3b968). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
R/transformCounts.R	82.85%	12 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##             devel     #614   +/-   ##
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  Coverage         ?   67.83%           
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  Files            ?       44           
  Lines            ?     5419           
  Branches         ?        0           
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  Hits             ?     3676           
  Misses           ?     1743           
  Partials         ?        0           

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[Daenarys8]

It seems css and css_fast is already in mia?
@TuomasBorman

[TuomasBorman]

It seems css and css_fast is already in mia? @TuomasBorman

It did not include the functionality; it included only "css" as one of the options. I am not sure how that ended up there, probably I copy-pasted the method-vector there incorrectly