Package org.snpsift

Class SnpSiftCmdCovarianceMatrix

  • All Implemented Interfaces:
    org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

    public class SnpSiftCmdCovarianceMatrix
    extends SnpSift
    Convert allele 'matrix' file into Covariance matrix Note: Only variants with two possible alleles. I.e. the matrix has three possible values in each cell: - 0, for allele 0/0 - 1, for allele 0/1 or 1/0 - 2, for allele 1/1
    Author:
    pcingola
    • Field Detail

      • SHOW_EVERY

        public static int SHOW_EVERY
    • Constructor Detail

      • SnpSiftCmdCovarianceMatrix

        public SnpSiftCmdCovarianceMatrix()
      • SnpSiftCmdCovarianceMatrix

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

      • covariance

        public void covariance()
        Calculate covariance matrix
      • mean

        public void mean()
        Calculate mean
      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Parse command line arguments
        Specified by:
        parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        parseArgs in class SnpSift
      • run

        public boolean run()
        Process the whole file
        Specified by:
        run in interface org.snpeff.snpEffect.commandLine.CommandLine
        Overrides:
        run in class SnpSift
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • 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
        Parameters:
        msg -