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
Count number of cases and controls
- Author:
- pablocingolani
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected Boolean[]
protected String
protected org.snpeff.ped.PedPedigree
protected double
static final int
protected String
protected boolean
static final String
static final String
static final String
static final String
static final String
static final String
static final String
Fields 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
Modifier and TypeMethodDescriptionboolean
annotate
(org.snpeff.vcf.VcfEntry vcfEntry) Annotate VCF entryprotected List
<org.snpeff.vcf.VcfHeaderEntry> headers()
Lines to be added to VCF headervoid
init()
Initialize default valuesprotected double
pAllelic
(int[] nControl, int[] nCase, double pvalueTh) Allelic model: Count number of SNPsvoid
Parse command line argumentsprotected double
pDominant
(int[] nControl, int[] nCase, double pvalueTh) Dominant model: Either a/A or A/A causes the diseaseprotected double
pGenotypic
(int[] nControl, int[] nCase) Genotypic model (Chi Square)protected double
pRecessive
(int[] nControl, int[] nCase, double pvalueTh) Recessive model: Only A/A causes the diseaseprotected String
processVcfHeader
(org.snpeff.fileIterator.VcfFileIterator vcf) Process VCF header related issuesprotected double
pTrend
(int[] nControl, int[] nCase) Trend modelboolean
run()
Load a file compare callsList
<org.snpeff.vcf.VcfEntry> run
(boolean createList) Runprotected void
swapMinorAllele
(int[] nControl, int[] nCase) Swap counts if REF is minor allele (instead of ALT)void
Show usage messageMethods inherited from class org.snpsift.SnpSift
addHeaders, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, isOpt, loadConfig, main, openVcfInputFile, 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 final int SHOW_EVERY- See Also:
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VCF_INFO_CASE
- See Also:
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VCF_INFO_CONTROL
- See Also:
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VCF_INFO_CC_GENO
- See Also:
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VCF_INFO_CC_ALL
- See Also:
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VCF_INFO_CC_DOM
- See Also:
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VCF_INFO_CC_REC
- See Also:
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VCF_INFO_CC_TREND
- See Also:
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caseControl
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tfamFile
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groups
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pedigree
protected org.snpeff.ped.PedPedigree pedigree -
pvalueThreshold
protected double pvalueThreshold -
useChiSquare
protected boolean useChiSquare
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Constructor Details
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SnpSiftCmdCaseControl
public SnpSiftCmdCaseControl() -
SnpSiftCmdCaseControl
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Method Details
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry) Annotate VCF entry -
headers
Lines to be added to VCF header -
init
public void init()Description copied from class:SnpSift
Initialize default values -
pAllelic
protected double pAllelic(int[] nControl, int[] nCase, double pvalueTh) Allelic model: Count number of SNPs -
parseArgs
Description copied from class:SnpSift
Parse command line arguments -
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
Description copied from class:SnpSift
Process VCF header related issues- Overrides:
processVcfHeader
in classSnpSift
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pTrend
protected double pTrend(int[] nControl, int[] nCase) Trend model -
run
public boolean run()Load a file compare calls -
run
Run- Parameters:
createList
- : Is true , create a list of VcfEntries (used in test cases)- Returns:
- A list of VcfEntry is createList is true
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swapMinorAllele
protected void swapMinorAllele(int[] nControl, int[] nCase) Swap counts if REF is minor allele (instead of ALT) -
usage
Show usage message
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