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Added information to the learn readme.

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Leandro Watanabe 2018-01-04 19:03:00 -07:00 • committed by GitHub
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learn/README.md
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@ -12,7 +12,7 @@ The learn project includes parameter estimation and a regulatory network learnin
After building the executable jar, you need to invoke the following command:
```
java -jar target/iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [-e] [-l ...] input directory
java -jar target/iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [options] input directory
```
where
@ -20,12 +20,34 @@ where
| Required | Description |
| ------------- | ------------- |
| ```input``` | arbitrary SBML file
| ```directory``` | location of the time-series data |
| input | arbitrary SBML file
| directory | location of the time-series data |
| Optional | Description |
| Options | Description |
| ------------- | ------------- |
| ```-e``` | perform parameter estimation. Default is GeneNet. |
```-l ...``` |a flag to specify which parameters need to be estimated, where the value is a comma separated list of parameter ids (e.g., "p1,p2,p3") |
| -e | perform parameter estimation. Default is GeneNet. |
| -l [list] | a flag to specify which parameters need to be estimated, where the value is a comma separated list of parameter ids (e.g., "p1,p2,p3") |
| -ta [num] | Sets the activation threshold. Default 1.15|
| -tr [num] | Sets the repression threshold. Default 0.75|
| -ti [num] | Sets how high a score must be to be considered a parent. Default 0.5|
| -tm [num] | Sets how close IVs must be in score to be considered for combination. Default 0.01|
| -tn [num] | Sets minimum number of parents to allow through in SelectInitialParents. Default 2|
| -tj [num] | Sets the max parents of merged influence vectors, Default 2|
| -tt [num] | Sets how fast the bound is relaxed for ta and tr, Default 0.025|
| -d [num] | Sets the debug or output level. Default 0|
| -wr [num] | Sets how much larger a number must be to be considered as a rise. Default 1|
| -ws [num] | Sets how far the TSD points are when compared. Default 1|
| -nb [num] | Sets how many bins are used in the evaluation. Default 4|
| --lvl | Writes out the suggested levels for every specie|
| --readLevels | Reads the levels from level.lvl file for every specie|
| --cpp_harshenBoundsOnTie | Determines if harsher bounds are used when parents tie in CPP.|
| --cpp_cmp_output_donotInvertSortOrder | Sets the inverted sort order in the 3 places back to normal|
| --cpp_seedParents | Determines if parents should be ranked by score, not tsd order in CPP.|
| --cmp_score_mustNotWinMajority | Determines if score should be used when following conditions are not met a > r+n || r > a + n|
| --score_donotTossSingleRatioParents | Determines if single ratio parents should be kept|
| --output_donotTossChangedInfluenceSingleParents | Determines if parents that change influence should not be tossed|
| -binNumbers | Equal spacing per bin|
| -noSUCC | to not use successors in calculating probabilities|
| -PRED | use preicessors in calculating probabilities|
| -basicFBP | to use the basic FindBaseProb function|