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 Boolean[]

caseControl

protected String

groups

protected org.snpeff.ped.PedPedigree

pedigree

protected double

pvalueThreshold

static final int

SHOW_EVERY

protected String

tfamFile

protected boolean

useChiSquare

static final String

VCF_INFO_CASE

static final String

VCF_INFO_CC_ALL

static final String

VCF_INFO_CC_DOM

static final String

VCF_INFO_CC_GENO

static final String

VCF_INFO_CC_REC

static final String

VCF_INFO_CC_TREND

static final 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(String[] args)
Method Summary

Modifier and Type

Method

Description

boolean

annotate(org.snpeff.vcf.VcfEntry vcfEntry)

Annotate VCF entry

protected 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(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 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

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(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 Details
- SHOW_EVERY
  
  public static final int SHOW_EVERY
  See Also:
  
  Constant Field Values
- VCF_INFO_CASE
  
  public static final String VCF_INFO_CASE
  See Also:
  
  Constant Field Values
- VCF_INFO_CONTROL
  
  public static final String VCF_INFO_CONTROL
  See Also:
  
  Constant Field Values
- VCF_INFO_CC_GENO
  
  public static final String VCF_INFO_CC_GENO
  See Also:
  
  Constant Field Values
- VCF_INFO_CC_ALL
  
  public static final String VCF_INFO_CC_ALL
  See Also:
  
  Constant Field Values
- VCF_INFO_CC_DOM
  
  public static final String VCF_INFO_CC_DOM
  See Also:
  
  Constant Field Values
- VCF_INFO_CC_REC
  
  public static final String VCF_INFO_CC_REC
  See Also:
  
  Constant Field Values
- VCF_INFO_CC_TREND
  
  public static final String VCF_INFO_CC_TREND
  See Also:
  
  Constant Field Values
- caseControl
  
  protected Boolean[] caseControl
- tfamFile
  
  protected String tfamFile
- groups
  
  protected String groups
- pedigree
  
  protected org.snpeff.ped.PedPedigree pedigree
- pvalueThreshold
  
  protected double pvalueThreshold
- useChiSquare
  
  protected boolean useChiSquare
Constructor Details
- SnpSiftCmdCaseControl
  
  public SnpSiftCmdCaseControl()
- SnpSiftCmdCaseControl
  
  public SnpSiftCmdCaseControl(String[] args)
Method Details
- 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 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(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 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 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(String msg)
  
  Show usage message
  
  Specified by:
  
  usage in interface org.snpeff.snpEffect.commandLine.CommandLine
  
  Overrides:
  
  usage in class SnpSift

Class SnpSiftCmdCaseControl

Field Summary

Fields inherited from class org.snpsift.SnpSift

Constructor Summary

Method Summary

Methods inherited from class org.snpsift.SnpSift

Methods inherited from class java.lang.Object

Field Details

SHOW_EVERY

VCF_INFO_CASE

VCF_INFO_CONTROL

VCF_INFO_CC_GENO

VCF_INFO_CC_ALL

VCF_INFO_CC_DOM

VCF_INFO_CC_REC

VCF_INFO_CC_TREND

caseControl

tfamFile

groups

pedigree

pvalueThreshold

useChiSquare

Constructor Details

SnpSiftCmdCaseControl

SnpSiftCmdCaseControl

Method Details

annotate

headers

init

pAllelic

parseArgs

pDominant

pGenotypic

pRecessive

processVcfHeader

pTrend

run

run

swapMinorAllele

usage