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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 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. 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: Options when making a Cell Sample file:
* Number of T cells to generate * Number of T cells to generate
* Factor by which CDR3s are more diverse than CDR1s * Factor by which CDR3s are more diverse than CDR1s
@@ -95,17 +97,13 @@ Comments are preceded by `#`
Structure: Structure:
--- ---
# Sample contains 1 unique CDR1 for every 4 unique CDR3s. # Sample contains 1 unique CDR1 for every 4 unique CDR3s.
| Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 | | Alpha CDR3 | Beta CDR3 | Alpha CDR1 | Beta CDR1 |
|---|---|---|---| |---|---|---|---|
|unique number|unique number|number|number| |unique number|unique number|number|number|
--- ---
**NOTE:** Matching of CDR1s is currently awaiting re-implementation.
#### Sample Plate Files #### Sample Plate Files
Sample Plate files consist of any number of "wells" containing any number of T cells (as 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 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 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. 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: Options for creating a Graph and Data file:
* The Cell Sample file to use * The Cell Sample file to use
* The Sample Plate file (generated from the given 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
Matching results files consist of the results of a BiGpairSEQ matching simulation. 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. 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 * given value from 0 to 100
* (To skip using this filter, enter 0) * (To skip using this filter, enter 0)
Sample File Structure: Example output:
--- ---
``` ```