Commit 0e48f417 authored by Menglin Zheng's avatar Menglin Zheng
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Update README.md

parent d1649e73
......@@ -35,17 +35,17 @@ The targets of perturbagen can be given by user or searched from the ChemPert da
4. **Perturbagen**: The perturbagen name from ChemPert database. If parameter 3 is given, this parameter should be NULL.
5. **Expression profile file**: Gene expression file of initial cellular state in rds/txt format, which contains the mean expression value for each genes (See example in `testdata/responseTFs_prediction_example/Expression_GSE162876_FPC_Adv_fibrosis.rds`).
5. **Expression profile file**: Gene expression file of initial cellular state in rds/txt format, which contains the mean expression value for each genes (See example in `testdata/responseTFs_prediction_example/Expression profile_GSE162876_FPC_Adv_fibrosis.rds`).
#### Run test dataset
```bash
Rscript pipeline_chempert.R 1 human ../testdata/responseTFs_prediction_example/obeticholic_acid_targets.rds NULL ../testdata/responseTFs_prediction_example/Expression_GSE162876_FPC_Adv_fibrosis.rds
Rscript pipeline_chempert.R 1 human ../testdata/responseTFs_prediction_example/obeticholic\ acid_targets.rds NULL ../testdata/responseTFs_prediction_example/Expression\ profile_GSE162876_FPC_Adv_fibrosis.rds
```
or
```bash
Rscript pipeline_chempert.R 1 human NULL "6-ecdca; 6-ethyl-cdca; 6-ethylchenodeoxycholic acid; 6alpha-ethyl-chenodeoxycholic acid; 6α-ethylchenodeoxycholic acid; obeticholic acid; ocaliva" ../testdata/responseTFs_prediction_example/Expression_GSE162876_FPC_Adv_fibrosis.rds
Rscript pipeline_chempert.R 1 human NULL "6-ecdca; 6-ethyl-cdca; 6-ethylchenodeoxycholic acid; 6alpha-ethyl-chenodeoxycholic acid; 6α-ethylchenodeoxycholic acid; obeticholic acid; ocaliva" ../testdata/responseTFs_prediction_example/Expression\ profile_GSE162876_FPC_Adv_fibrosis.rds
```
#### Option 2: The prediction of perturbagens
......
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