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meyer-lab / FcRegression.jl

Study Fc antibody dynamics using a multivalent binding model
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Manuscript #294

Closed stephendl102 closed 3 years ago

stephendl102 commented 3 years ago

@aarmey I noticed the build failed, and I believe its because it timed out after 6 hours. I knew the fitting would make it take longer, but I didn't know it would take that long. Is there something we can do about this? Or is there an error somewhere that you could point me to?

aarmey commented 3 years ago

What specifically is changing here? I see a ton of changes, so I'm not really sure what to look at.

stephendl102 commented 3 years ago

@aarmey There are a few differences. The first is that I edited the manuscript. Second, I added a figure 4 to build for the manuscript. Third, I provided an upper and lower bound for fit activity so that fitRegression() actually fits the activity rather than just using the constant vector; this allows the synergy plots to be formed based off of fit activities depending on the disease model. Lastly, I allowed optional arguments for many of the functions to allow for specification of single receptors, single cell type, disease type, receptor binding/induced activity/depletion. I just reduced the upper and lower bounds from five to four in the hopes that this would allow the figures to build faster.

aarmey commented 3 years ago

These should be separate pull requests because they do different things. This will also help to uncover what the problem is.

codecov-io commented 3 years ago

Codecov Report

Merging #294 (2730a26) into master (3e39c74) will decrease coverage by 19.02%. The diff coverage is 0.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #294       +/-   ##
==========================================
- Coverage   28.15%   9.12%   -19.03%     
==========================================
  Files          19      20        +1     
  Lines         927     986       +59     
==========================================
- Hits          261      90      -171     
- Misses        666     896      +230
Impacted Files Coverage Δ
src/FcRegression.jl 3.22% <0.00%> (-0.11%) :arrow_down:
src/fcBindingModel.jl 0.00% <ø> (-76.48%) :arrow_down:
src/figures/figure4.jl 0.00% <0.00%> (ø)
src/figures/figureB1.jl 0.00% <0.00%> (ø)
src/figures/figureDiseaseSynergy.jl 0.00% <0.00%> (ø)
src/figures/figureS.jl 0.00% <ø> (ø)
src/figures/figureW.jl 0.00% <0.00%> (ø)
src/regression.jl 0.00% <0.00%> (-96.65%) :arrow_down:
src/synergy.jl 0.00% <0.00%> (ø)
... and 4 more

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