R/R_myOR.CI3.r

In CGEN: An R package for analysis of case-control studies in genetic epidemiology

  #### 5/6/2010 take out arguments for  Estimate Std. Error    z value     Pr(>|z|)
 
  #bNames="Estimate"
  #sdName="Std. Error"
  #pName="Pr(>|z|)"
  
  myOR.CI3=function(xx,bName="Estimate",sName="Std. Error",pName="Pr(>|z|)",pval=F){

        #> xx=full$coef
        #> xx
        #                Estimate Std. Error    z value     Pr(>|z|)
        #(Intercept) -0.750026027 0.14114317 -5.3139379 1.072812e-07
        #geno         0.168774184 0.04662121  3.6201160 2.944709e-04
        #race1        0.297560013 0.10316615  2.8842796 3.923103e-03
        #sex1        -0.073478696 0.07416867 -0.9906972 3.218334e-01
        #age_cat1    -0.113698897 0.10863623 -1.0466020 2.952832e-01
        #age_cat2    -0.138700275 0.10581389 -1.3107945 1.899272e-01
        #age_cat3    -0.309324107 0.10913423 -2.8343453 4.591968e-03
        #age_cat4    -0.263627342 0.11893800 -2.2165106 2.665655e-02
        #age_cat5    -0.263389923 0.23039374 -1.1432165 2.529487e-01
        #smoking1     0.135488073 0.23874607  0.5674986 5.703754e-01
        #smoking2    -0.002006010 0.08506604 -0.0235818 9.811862e-01
        #smoking3    -0.373251080 0.08498864 -4.3917760 1.124285e-05
        #bmi1         0.169979498 0.08502958  1.9990631 4.560153e-02
        #bmi2         0.303177546 0.09434804  3.2133953 1.311756e-03
        #bmi3         0.579843176 0.11796522  4.9153741 8.861307e-07
        #everhbp1     0.583651325 0.06945305  8.4035372 4.332274e-17

        #tm1=as.vector(xx[,"Estimate"])
        #tm2=as.vector(xx[,"Std. Error"])
        #tm3=as.vector(xx[,"Pr(>|z|)"])
        
        tm1=as.vector(xx[,bName])
        tm2=as.vector(xx[,sName])
        tm3=as.vector(xx[,pName])
                
        OR=exp(tm1)
        CI0=cbind(tm1-1.96*tm2,tm1+1.96*tm2)
        CI=exp(CI0)

        #> OR
        # [1] 0.4723543 1.1838528 1.3465692 0.9291559 0.8925267 0.8704889 0.7339429
        # [8] 0.7682598 0.7684422 1.1450955 0.9979960 0.6884923 1.1852806 1.3541549
        #[15] 1.7857584 1.7925718
        #> CI
        #           [,1]      [,2]
        # [1,] 0.3581990 0.6228900
        # [2,] 1.0804705 1.2971269
        # [3,] 1.1000486 1.6483350
        # [4,] 0.8034428 1.0745392
        # [5,] 0.7213535 1.1043182
        # [6,] 0.7074449 1.0711094
        # [7,] 0.5926050 0.9089902
        # [8,] 0.6085076 0.9699518
        # [9,] 0.4892109 1.2070530
        #[10,] 0.7171615 1.8283801
        #[11,] 0.8447323 1.1790670
        #[12,] 0.5828480 0.8132853
        #[13,] 1.0033270 1.4002314
        #[14,] 1.1255315 1.6292173
        #[15,] 1.4171267 2.2502808
        #[16,] 1.5644328 2.0539799
        
        ans=cbind(OR=OR,CI1=CI[,1],CI2=CI[,2],beta=tm1,sd=tm2)
        
        
        if(pval==T){
        ans=cbind(OR=OR,CI1=CI[,1],CI2=CI[,2],beta=tm1,sd=tm2,pval2=tm3)
        
        }
        
        
        ans

   }# end of myOR.CI