hpo_similarity

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Analysis of similarity of HPO terms in groups of individuals

hpo_similarity 최신버젼 다운로드

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#### Similarity of phenotypes in patient groups
This estimates how likely it is for groups of individuals to have similar
phenotypes.  To estimate this probability, we need three things:
- a way to quantify phenotypic similarity of two individuals. We use the maximum
  information content of the most informative common ancestor for each pair of
  HPO terms from two probands.
- a way to quantify similarity across more than two probands. We sum phenotypic
  similarity scores from all pairs of probands.
- a null distribution of similarity scores for those probands, generated by
  randomly sampled groups of probands

The P value is calculated as the proportion of simulated scores greater than the
observed probands' score.

##### Install
Install the package with:
```sh
pip install hpo_similarity
```

##### Run
```sh
hpo_similarity --genes genes.json --phenotypes phenotypes.json
```
The data directory on github includes example files, one with proband IDs
per gene ([data/example_genes.json](data/example_genes.json)), and the other
with HPO terms per proband ([data/example_phenotypes.json](data/example_phenotypes.json)).

Additional options:
- `--output PATH` to send output gene and P-values to a file.
- `--ontology PATH` to use a HPO ontology file other than the default.
- `--iterations INTEGER` to change the number of iterations (default=100000)

You can also explore the HPO graph using the hpo_similarity package within
python, for example:
```python
from hpo_similarity import open_ontology

graph, alt_ids, obsolete_ids = open_ontology()

# find all descendant terms
graph.get_descendants('HP:0001249')

# get the text for the phenotypic abnormality
graph.nodes['HP:0001249']['name']
```

##### Acknowledgments
  This code incorporates the following code and datasets:
  - a [python ontology parser](https://github.com/ntamas/gfam/blob/master/gfam/go/obo.py)
    written by Tamás Nepusz.
  - the [hp.obo file](http://purl.obolibrary.org/obo/hp.obo) from the
    [Human Phenotype Ontology Consortium](http://human-phenotype-ontology.org/).

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