Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib

opencb / hpg-bigdata

This repository implements converters and tools for working with NGS data in HPC or Hadoop cluster

Apache License 2.0

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Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib #126

Open jtarraga opened 7 years ago

jtarraga commented 7 years ago

The package should provide variant association analysis such as chi-square, linear and logistic regression. Spark's Machine Learning library (MLlib) provides a rich API to implement them in a bigdata environment.

Association tests:

[ ] Chi-square
[ ] Logistic regression
[ ] Linear regression

Taking into account the following genetic models:

[ ] Dominant
[ ] Recessive
[ ] Additive effects of allele dosage