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improve documentation

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efischer
2022-02-20 17:11:39 -06:00
parent 24519f4a52
commit 405fbf17ff
1 changed files with 8 additions and 10 deletions
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readme.md
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@@ -85,6 +85,8 @@ four sequences: Alpha CDR3, Beta CDR, Alpha CDR1, Beta CDR1. The sequences are r
random integers. CDR3 Alpha and Beta sequences are all unique. CDR1 Alpha and Beta sequences
are not necessarily unique; the relative diversity can be set when making a Cell Sample file.
(Note: though cells still have CDR1 sequences, matching of CDR1s is currently awaiting re-implementation.)
Options when making a Cell Sample file:
* Number of T cells to generate
* Factor by which CDR3s are more diverse than CDR1s
@@ -95,17 +97,13 @@ Comments are preceded by `#`
Structure:
---
# Sample contains 1 unique CDR1 for every 4 unique CDR3s.
| Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
|---|---|---|---|
|unique number|unique number|number|number|
---
**NOTE:** Matching of CDR1s is currently awaiting re-implementation.
#### Sample Plate Files
Sample Plate files consist of any number of "wells" containing any number of T cells (as
described above). The wells are filled randomly from a Cell Sample file, according to a selected
@@ -163,15 +161,15 @@ the accuracy of BiGpairSEQ simulations) and a Sample Plate file (to construct th
occupancy graph). These files can be several gigabytes in size. Writing them to a file lets us generate a graph and
its metadata once, then use it for multiple different BiGpairSEQ simulations.
These files do not have a human-readable structure, and are not portable to other programs.
(Export of graphs in a portable data format may be implemented in the future.
Exporting the graph itself is easy, the tricky part is packaging it with the necessary metadata.)
Options for creating a Graph and Data file:
* The Cell Sample file to use
* The Sample Plate file (generated from the given Cell Sample file) to use.
These files do not have a human-readable structure, and are not portable to other programs. (Export of graphs in a
portable data format may be implemented in the future. The tricky part is encoding the necessary metadata.)
---
#### Matching Results Files
Matching results files consist of the results of a BiGpairSEQ matching simulation.
Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
@@ -188,7 +186,7 @@ Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching:
* given value from 0 to 100
* (To skip using this filter, enter 0)
Sample File Structure:
Example output:
---
```