A Genetic Analysis Package with R.pdf

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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.Ihopeeventuallythiswillbepartofabiggereorttoful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/Powercalculationformediatingeectaldh2ALDH2markersandalcoholismapoeapocAPOE/APOC1markersandschizophreniaasplotRegionalassociationplotbtBradley-Terrymodelforcontingencytableb2rObtaincorrelationcoecientsandtheirvar

7、iance-covariancesccsizePowerandsamplesizeforcase-cohortdesignchow.testChow'stestforheterogeneityintworegressionscfCysticFibrosisdatacomp.scorescorestatisticsfortestinggeneticlinkageofquantitativetraitcrohnCrohn'sdiseasedataESplotEect-sizeplotfaFriedreic