Comments (2)
Python API for generic variant-spark interface.
Should be implemented in variants
module in python
directory.
The main access point should be VariantsContext
which can be used to load features and labels.
The API should be based on the 'non-depricated' scala api (from au.csiro.variantspark.api)
The general use pattern should he like this
from variants import VariantsContext
vc = VariantsContext(spark)
features = vc.import_vcf(input_path = "path-to-a-vcf-file")
label = vs.load_label(input_path = "path-to-a-csv_file", col_name = "column-name)
imp_analysis = features.importance_analysis(label, n_trees = 1000, m_try_fraction = 0.1, ...)
oob_error = imp_analysis.oob_error
imp_vars_df = imp_analysis.important_variables()
# imp_vars_df is a spark.sql.DataFrame
Some guidance on the implementation can be found in the variants.hail
module.
from variantspark.
API implemented.
Some technical debts reported as new issues.
from variantspark.
Related Issues (20)
- Make pull request to hail with jar config changes.
- Align python code formatting between pylind and inteliJ
- Additional support for prediction HOT 1
- Update the Cloud Marketplace example Notebooks to include logistic regression covariates HOT 1
- Make the covariate calculation part of RF HOT 3
- Improve release and versioning HOT 1
- Grid Search for Parameter Optimisation HOT 1
- add p-value calculation to HAIL implementation
- Add variable count extraction from json model
- Migrate to Spark 3.1 HOT 1
- automate pvalue calculation in VariantSpark pipeline
- optimise VariantSpark for large sample size (n>50K) HOT 1
- Add split variable count to hail output
- Integrate python build with maven and revise deployment with github actions.
- How to use vcf file? HOT 4
- HADOOP ERROR SERVICE AWS.... HOT 9
- run on single chromosomes? HOT 1
- Can we remove the Hail monkey patches after this Hail PR? HOT 1
- fit_trees() unable to run due to IncompatibleClassChangeError HOT 2
- Reporting a vulnerability
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from variantspark.