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Add data on randomized well population behavior

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efischer
2022-03-02 18:55:19 -06:00
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@@ -279,6 +279,49 @@ Since this implementation of BiGpairSEQ writes intermediate results to disk (to
with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took
slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes.
## BEHAVIOR WITH RANDOMIZED WELL POPULATIONS
A series of BiGpairSEQ simulations were conducted using a cell sample file of 3.5 million unique T cells. From these cells,
10 sample plate files were created. All of these sample plates had 96 wells, used an exponential distribution with a lambda of 0.6, and
had a sequence dropout rate of 10%.
The well populations of the plates were:
* One sample plate with 1000 T cells/well
* One sample plate with 2000 T cells/well
* One sample plate with 3000 T cells/well
* One sample plate with 4000 T cells/well
* One sample plate with 5000 T cells/well
* Five sample plates with each individual well's population randomized, from 1000 to 5000 T cells. (Average population ~3000 T cells/well.)
All BiGpairSEQ simulations were run with a low overlap threshold of 3 and a high overlap threshold of 94.
Constant well population plate results:
| |1000 Cell/Well Plate|2000 Cell/Well Plate|3000 Cell/Well Plate|4000 Cell/Well Plate|5000 Cell/Well Plate
|---|---|---|---|---|---|
|Total Alphas Found|6407|7330|7936|8278|8553|
|Total Betas Found|6405|7333|7968|8269|8582|
|Pairing Attempt Rate|0.661|0.653|0.600|0.579|0.559|
|Correct Pairing Count|4231|4749|4723|4761|4750|
|Incorrect Pairing Count|3|34|40|26|29|
|Pairing Error Rate|0.000709|0.00711|0.00840|0.00543|0.00607|
|Simulation Time (Seconds)|500|643|700|589|598|
Randomized well population plate results:
| |Random Plate 1 | Random Plate 2|Random Plate 3|Random Plate 4|Random Plate 5|Average|
|---|---|---|---|---|---|---|
Total Alphas Found|7853|7904|7964|7898|7917|7907|
Total Betas Found|7851|7891|7920|7910|7894|7893|
Pairing Attempt Rate|0.607|0.610|0.601|0.605|0.603|0.605|
Correct Pairing Count|4718|4782|4721|4755|4731|4741|
Incorrect Pairing Count|51|35|42|27|29|37|
Pairing Error Rate|0.0107|0.00727|0.00882|0.00565|0.00609|0.00771|
Simulation Time (Seconds)|590|677|730|618|615|646|
From these results, it can be seen that BiGpairSEQ treats a sample plate with a highly variable number of T cells/well
roughly as though it had a constant well population equal to the average well population.
## TODO
* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE