variantspark

Value Members

1. package algo

   

2. package api

   

   Provides API for Variant Spark.

   Provides API for Variant Spark.

   Overview

   The main class to use is au.csiro.variantspark.VSContext, as so

   import au.csiro.variantspark.api._
   implicit val vsContext = VSContext(spark)
   val features = vsContext.importVCF("data/chr22_1000.vcf")
   val label = vsContext.loadLabel("data/chr22-labels.csv", "22_16050408")
   val impAnalysis = features.importanceAnalysis(label, nTrees = 100, seed = Some(13L))
   // retrieve top 20 variables as a Seq
   val top20Variables = impAnalysis.importantVariables(20)
   // or retrieve all of them as a DataFram
   val variableDF = impAnalysis.variableImportance

3. package cli

   

4. package cmd

   

5. package data

   

6. package genomics

   

7. package hail

   

8. package input

   

9. package metrics

   

10. package output

    

11. package stats

    

12. package tests

    

13. package utils

    

14. package work