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

public class SnpSiftCmdCaseControl
extends SnpSift

Count number of cases and controls

Author:

pablocingolani

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

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

Constructor Summary

Constructors

Constructor	Description
SnpSiftCmdCaseControl()
SnpSiftCmdCaseControl(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
boolean	annotate(org.snpeff.vcf.VcfEntry vcfEntry)	Annotate VCF entry
protected java.util.List<org.snpeff.vcf.VcfHeaderEntry>	headers()	Lines to be added to VCF header
void	init()	Initialize default values
protected double	pAllelic(int[] nControl, int[] nCase, double pvalueTh)	Allelic model: Count number of SNPs
void	parseArgs(java.lang.String[] args)	Parse command line arguments
protected double	pDominant(int[] nControl, int[] nCase, double pvalueTh)	Dominant model: Either a/A or A/A causes the disease
protected 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 disease
protected java.lang.String	processVcfHeader(org.snpeff.fileIterator.VcfFileIterator vcf)	Process VCF header related issues
protected double	pTrend(int[] nControl, int[] nCase)	Trend model
boolean	run()	Load a file compare calls
java.util.List<org.snpeff.vcf.VcfEntry>	run(boolean createList)	Run
protected 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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SHOW_EVERY

public static final int SHOW_EVERY

See Also:

Constant Field Values

VCF_INFO_CASE

public static final java.lang.String VCF_INFO_CASE

See Also:

Constant Field Values

VCF_INFO_CONTROL

public static final java.lang.String VCF_INFO_CONTROL

See Also:

Constant Field Values

VCF_INFO_CC_GENO

public static final java.lang.String VCF_INFO_CC_GENO

See Also:

Constant Field Values

VCF_INFO_CC_ALL

public static final java.lang.String VCF_INFO_CC_ALL

See Also:

Constant Field Values

VCF_INFO_CC_DOM

public static final java.lang.String VCF_INFO_CC_DOM

See Also:

Constant Field Values

VCF_INFO_CC_REC

public static final java.lang.String VCF_INFO_CC_REC

See Also:

Constant Field Values

VCF_INFO_CC_TREND

public static final java.lang.String VCF_INFO_CC_TREND

See Also:

Constant Field Values

caseControl

protected java.lang.Boolean[] caseControl

tfamFile

protected java.lang.String tfamFile

groups

protected java.lang.String groups

pedigree

protected org.snpeff.ped.PedPedigree pedigree

pvalueThreshold

protected double pvalueThreshold

useChiSquare

protected boolean useChiSquare

Constructor Detail

SnpSiftCmdCaseControl

public SnpSiftCmdCaseControl()

SnpSiftCmdCaseControl

public SnpSiftCmdCaseControl(java.lang.String[] args)

Method Detail

annotate

public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)

Annotate VCF entry

Specified by:

annotate in interface org.snpeff.snpEffect.VcfAnnotator

Overrides:

annotate in class SnpSift

headers

protected java.util.List<org.snpeff.vcf.VcfHeaderEntry> headers()

Lines to be added to VCF header

Overrides:

headers in class SnpSift

init

public void init()

Description copied from class: SnpSift

Initialize default values

Overrides:

init in class SnpSift

pAllelic

protected double pAllelic(int[] nControl,
                          int[] nCase,
                          double pvalueTh)

Allelic model: Count number of SNPs

parseArgs

public void parseArgs(java.lang.String[] args)

Description copied from class: SnpSift

Parse command line arguments

Specified by:

parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

parseArgs in class SnpSift

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

protected java.lang.String processVcfHeader(org.snpeff.fileIterator.VcfFileIterator vcf)

Description copied from class: SnpSift

Process VCF header related issues

Overrides:

processVcfHeader in class SnpSift

pTrend

protected double pTrend(int[] nControl,
                        int[] nCase)

Trend model

run

public boolean run()

Load a file compare calls

Specified by:

run in interface org.snpeff.snpEffect.commandLine.CommandLine

Overrides:

run in class SnpSift

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

swapMinorAllele

protected void swapMinorAllele(int[] nControl,
                               int[] nCase)

Swap counts if REF is minor allele (instead of ALT)

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