Package org.snpsift
Class SnpSiftCmdCaseControl
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdCaseControl
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- 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
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Field Summary
Fields Modifier and Type Field Description protected java.lang.Boolean[]
caseControl
protected java.lang.String
groups
protected org.snpeff.ped.PedPedigree
pedigree
protected double
pvalueThreshold
static int
SHOW_EVERY
protected java.lang.String
tfamFile
protected boolean
useChiSquare
static java.lang.String
VCF_INFO_CASE
static java.lang.String
VCF_INFO_CC_ALL
static java.lang.String
VCF_INFO_CC_DOM
static java.lang.String
VCF_INFO_CC_GENO
static java.lang.String
VCF_INFO_CC_REC
static java.lang.String
VCF_INFO_CC_TREND
static java.lang.String
VCF_INFO_CONTROL
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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 Constructor Description SnpSiftCmdCaseControl()
SnpSiftCmdCaseControl(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
annotate(org.snpeff.vcf.VcfEntry vcfEntry)
Annotate VCF entryprotected java.util.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
parseArgs(java.lang.String[] args)
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 java.lang.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 callsjava.util.List<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
usage(java.lang.String msg)
Show usage message-
Methods 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 Detail
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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VCF_INFO_CASE
public static final java.lang.String VCF_INFO_CASE
- See Also:
- Constant Field Values
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VCF_INFO_CONTROL
public static final java.lang.String VCF_INFO_CONTROL
- See Also:
- Constant Field Values
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VCF_INFO_CC_GENO
public static final java.lang.String VCF_INFO_CC_GENO
- See Also:
- Constant Field Values
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VCF_INFO_CC_ALL
public static final java.lang.String VCF_INFO_CC_ALL
- See Also:
- Constant Field Values
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VCF_INFO_CC_DOM
public static final java.lang.String VCF_INFO_CC_DOM
- See Also:
- Constant Field Values
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VCF_INFO_CC_REC
public static final java.lang.String VCF_INFO_CC_REC
- See Also:
- Constant Field Values
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VCF_INFO_CC_TREND
public static final java.lang.String VCF_INFO_CC_TREND
- See Also:
- Constant Field Values
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caseControl
protected java.lang.Boolean[] caseControl
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tfamFile
protected java.lang.String tfamFile
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groups
protected java.lang.String groups
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pedigree
protected org.snpeff.ped.PedPedigree pedigree
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pvalueThreshold
protected double pvalueThreshold
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useChiSquare
protected boolean useChiSquare
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Method Detail
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
Annotate VCF entry
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headers
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()
Lines to be added to VCF header
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init
public void init()
Description copied from class:SnpSift
Initialize default values
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pAllelic
protected double pAllelic(int[] nControl, int[] nCase, double pvalueTh)
Allelic model: Count number of SNPs
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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from class:SnpSift
Parse command line arguments
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pDominant
protected double pDominant(int[] nControl, int[] nCase, double pvalueTh)
Dominant model: Either a/A or A/A causes the disease
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pGenotypic
protected double pGenotypic(int[] nControl, int[] nCase)
Genotypic model (Chi Square)
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pRecessive
protected double pRecessive(int[] nControl, int[] nCase, double pvalueTh)
Recessive model: Only A/A causes the disease
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processVcfHeader
protected java.lang.String processVcfHeader(org.snpeff.fileIterator.VcfFileIterator vcf)
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
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run
public boolean run()
Load a file compare calls
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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
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swapMinorAllele
protected void swapMinorAllele(int[] nControl, int[] nCase)
Swap counts if REF is minor allele (instead of ALT)
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