Comments (1)
@BauerLab as far as I can tell they are already included in the example notebook see: https://bitbucket.csiro.au/users/hos076/repos/variantspark-aws/browse/data/monitor-ami/notebook/VariantSpark_example.ipynb
(or : https://variantspark-marketplace-resources.s3.amazonaws.com/static/public/example_notebook.html)
covariates = [mt.pheno.isFemale, mt.pcs[0], mt.pcs[1]]
result = hl.logistic_regression_rows(test ='wald',
y=mt.pheno.isCase,
x=mt.GT.n_alt_alleles(),
covariates=covariates)
Also as the code for AWS deployment is managed in different repository I think it would be better to manage the related issue somewhere else, unless they do require changes in the core variant spark.
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Related Issues (20)
- Additional support for prediction 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
- Install on our supercomputer throws ```java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class au/csiro/pbdava/ssparkle/spark/SparkApp. Method 'java.lang.String $anonfun$spark$1(au.csiro.pbdava.ssparkle.spark.SparkApp)' at index 118 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef``` HOT 1
- Install on any machine throws ``` java.lang.IncompatibleClassChangeError``` HOT 1
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