Package org.snpsift

Class SnpSiftCmdCovarianceMatrix

java.lang.Object
org.snpsift.SnpSift
org.snpsift.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 Details

    • SHOW_EVERY

      public static int SHOW_EVERY
  • Constructor Details

    • SnpSiftCmdCovarianceMatrix

      public SnpSiftCmdCovarianceMatrix()
    • SnpSiftCmdCovarianceMatrix

      public SnpSiftCmdCovarianceMatrix(String[] args)
  • Method Details

    • covariance

      public void covariance()
      Calculate covariance matrix
    • mean

      public void mean()
      Calculate mean
    • parseArgs

      public void parseArgs(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 String toString()
      Overrides:
      toString in class Object
    • usage

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