Package org.snpsift

Class 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 Detail

      • VCF_INFO_CONTROL

        public static final java.lang.String VCF_INFO_CONTROL
        See Also:
        Constant Field Values
      • VCF_INFO_CC_GENO

        public static final java.lang.String VCF_INFO_CC_GENO
        See Also:
        Constant Field Values
      • VCF_INFO_CC_TREND

        public static final java.lang.String VCF_INFO_CC_TREND
        See Also:
        Constant Field Values
      • caseControl

        protected java.lang.Boolean[] caseControl
      • tfamFile

        protected java.lang.String tfamFile
      • groups

        protected java.lang.String groups
      • pedigree

        protected org.snpeff.ped.PedPedigree pedigree
      • pvalueThreshold

        protected double pvalueThreshold
      • useChiSquare

        protected boolean useChiSquare
    • Constructor Detail

      • SnpSiftCmdCaseControl

        public SnpSiftCmdCaseControl()
      • SnpSiftCmdCaseControl

        public SnpSiftCmdCaseControl​(java.lang.String[] args)
    • Method Detail

      • 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 java.util.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​(java.lang.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 java.lang.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 java.util.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​(java.lang.String msg)
        Show usage message
        Specified by:
        usage in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        usage in class SnpSift