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
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
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Field Summary
FieldsFields inherited from class org.snpsift.SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class org.snpsift.SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, init, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb
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Field Details
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SHOW_EVERY
public static int SHOW_EVERY
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Constructor Details
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SnpSiftCmdCovarianceMatrix
public SnpSiftCmdCovarianceMatrix() -
SnpSiftCmdCovarianceMatrix
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Method Details
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covariance
public void covariance()Calculate covariance matrix -
mean
public void mean()Calculate mean -
parseArgs
Parse command line arguments -
run
public boolean run()Process the whole file -
toString
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usage
Show usage message
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