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1、AGeneticAnalysisPackagewithRJingHuaZhaoMRCEpidemiologyUnit,Cambridge,UKhttp://www.mrc-epid.cam.ac.ukContents1Introduction12Implementation23Demos44Examples44.1Studydesign.....................................44.2Kinshipcalculation..................................94.3Graphicsexamples.........
2、.........................155Knownbugs196Bibliographicnote191IntroductionThispackagewasinitiatedtointegratesomeC/Fortran/SASprogramsIhavewrittenorusedovertheyears.Assuch,itwouldratherbealong-termproject,butanimmediatebene twouldbesomethingcomplementarytootherpackagescurrentlyavailablefromCRA
3、N,e.g.genetics,hwde,etc.Ihopeeventuallythiswillbepartofabiggere orttoful llmostoftherequirementsforeseenbymany,e.g.GuoandLange(2000),withintheportableenviron-mentofRfordatamanagement,analysis,graphicsandobject-orientedprogramming.MyviewhasbeenoutlinedmoreformallyinZhaoandTan(2006a)andZhaoan
4、dTan(2006b)inrelationtootherpackagesystems.AlsoreportedareZhao(2005)andZhao(2006)onpackagekinship.Thenumberoffunctionsarequitelimitedandexperimental,butIalreadyfeeltheenormousadvantagebyshiftingtoRandwouldlikesoonerratherthanlatertosharemyworkwithothers.Iwillnotclaimthisworkasexclusivelydon
5、ebyme,butwouldliketoinviteotherstojoinmeandenlargethecollectionsandimprovethem.12ImplementationThefollowinglistshowsthedataandfunctionscurrentlyavailable.AE3AEmodelusingnuclearfamilytriosBFDPBayesianfalse-discoveryprobabilityFPRPFalse-positivereportprobabilityPDAstudyofParkinson'sdiseaseand
6、APOE,LRRK2,SNCAmakersSNPFunctionsforsinglenucleotidepolymorphisms(SNPs)abTest/Powercalculationformediatinge ectaldh2ALDH2markersandalcoholismapoeapocAPOE/APOC1markersandschizophreniaasplotRegionalassociationplotbtBradley-Terrymodelforcontingencytableb2rObtaincorrelationcoecientsandtheirvar
7、iance-covariancesccsizePowerandsamplesizeforcase-cohortdesignchow.testChow'stestforheterogeneityintworegressionscfCysticFibrosisdatacomp.scorescorestatisticsfortestinggeneticlinkageofquantitativetraitcrohnCrohn'sdiseasedataESplotE ect-sizeplotfaFriedreic
