Package org.snpsift

Class SnpSiftCmdCaseControl

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdCaseControl
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdCaseControl extends SnpSift
Count number of cases and controls
Author:
pablocingolani
  • Field Details

  • Constructor Details

    • SnpSiftCmdCaseControl

      public SnpSiftCmdCaseControl()
    • SnpSiftCmdCaseControl

      public SnpSiftCmdCaseControl(String[] args)
  • Method Details

    • annotate

      public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
      Annotate VCF entry
      Specified by:
      annotate in interface org.snpeff.snpEffect.VcfAnnotator
      Overrides:
      annotate in class SnpSift
    • headers

      protected List<org.snpeff.vcf.VcfHeaderEntry> headers()
      Lines to be added to VCF header
      Overrides:
      headers in class SnpSift
    • init

      public void init()
      Description copied from class: SnpSift
      Initialize default values
      Overrides:
      init in class SnpSift
    • pAllelic

      protected double pAllelic(int[] nControl, int[] nCase, double pvalueTh)
      Allelic model: Count number of SNPs
    • parseArgs

      public void parseArgs(String[] args)
      Description copied from class: SnpSift
      Parse command line arguments
      Specified by:
      parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      parseArgs in class SnpSift
    • pDominant

      protected double pDominant(int[] nControl, int[] nCase, double pvalueTh)
      Dominant model: Either a/A or A/A causes the disease
    • pGenotypic

      protected double pGenotypic(int[] nControl, int[] nCase)
      Genotypic model (Chi Square)
    • pRecessive

      protected double pRecessive(int[] nControl, int[] nCase, double pvalueTh)
      Recessive model: Only A/A causes the disease
    • processVcfHeader

      protected String processVcfHeader(org.snpeff.fileIterator.VcfFileIterator vcf)
      Description copied from class: SnpSift
      Process VCF header related issues
      Overrides:
      processVcfHeader in class SnpSift
    • pTrend

      protected double pTrend(int[] nControl, int[] nCase)
      Trend model
    • run

      public boolean run()
      Load a file compare calls
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift
    • run

      public List<org.snpeff.vcf.VcfEntry> run(boolean createList)
      Run
      Parameters:
      createList - : Is true , create a list of VcfEntries (used in test cases)
      Returns:
      A list of VcfEntry is createList is true
    • swapMinorAllele

      protected void swapMinorAllele(int[] nControl, int[] nCase)
      Swap counts if REF is minor allele (instead of ALT)
    • usage

      public void usage(String msg)
      Show usage message
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift