Nothing
R/R_makeBetaTable.general.r
In CGEN: An R package for analysis of case-control studies in genetic epidemiology
Defines functions
makeBetaTable.general
makeBetaTable.general=function(betas,method){ ## this construct beta table out of beta coefficient
coeff=betas # betas should include b0
if (method=="2x2" | length(grep("2by2",method))!=0) {
#> vc
# (Intercept) xx11 xx21 xx11:xx21
#(Intercept) 0.007147387 -0.007147387 -0.007147387 0.007147387
#xx11 -0.007147387 0.012507390 0.007147387 -0.012507390
#xx21 -0.007147387 0.007147387 0.010774803 -0.010774803
#xx11:xx21 0.007147387 -0.012507390 -0.010774803 0.018271530
#vars=diag(vc)
#> vars
#(Intercept) xx11 xx21 xx11:xx21
#0.007147387 0.012507390 0.010774803 0.018271530
# b0 b1 b2 b3
# 1 2 3 4
# table is:
# b0 b0+b2 1 1+3
# b0+b1 b0+b1+b2+b3 1+2 1+2+3+4
#
#ans1=rep(NA,4) # total 2 by 2 = 4 cells
ans2=rep(NA,4)
for(j in 1:length(ans2)){
if(j==1) nums=1
if(j==2) nums=c(1,3)
if(j==3) nums=c(1,2)
if(j==4) nums=c(1,2,3,4)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
tb.b=matrix(ans2,byrow=T,nrow=2) # inverse of variance
tb.b
# [,1] [,2] [,3]
#[1,] 139.91126 228.6460 29.81521
#[2,] 142.15404 321.5600 38.28501
#[3,] 26.62504 42.6484 6.09793
}#end of
if (method=="3x3" | length(grep("3by3",method))!=0) { # if 3 by 3 table model
#vars
#(Intercept) xx11 xx12 xx21 xx22 xx11:xx21 xx12:xx21 xx11:xx22 xx12:xx22
#0.007147387 0.014182010 0.030524010 0.011520961 0.029166356 0.021665423 0.050861708 0.052176401 0.117532487
# b0 bg1 bg2 bx1 bx2 d11 d21 d12 d22
# 1 2 3 4 5 ( 6 7 8 9 )
# table is: 0 1 2
# 0 b0 b0+bx1 b0+bx2
# 1 b0+bg1 b0+bg1+bx1+d11 b0+bg1+bx2+d12
# 2 b0+bg2 b0+bg2+bx1+d21 b0+bg2+dx2+d22
# ------> 1 1+4 1+5
# 1+2 1+2+4+6 1+2+5+8
# 1+3 1+3+4+7 1+3+5+9
#coeff
#(Intercept) xx11 xx12 xx21 xx22 xx11:xx21 xx12:xx21 xx11:xx22 xx12:xx22
# -1.2012218 0.2669125 0.7492366 1.0790657 0.6657035 0.7198954 0.1653648 0.6580705 1.5593489
# 1 2 3 4 5 (6 7 8 9)
#ans1=rep(NA,9) # total 3 by 3 = 9 cells
ans2=rep(NA,9) # total 3 by 3 = 9 cells
for(j in 1:length(ans2)){
if(j==1) nums=1
if(j==2) nums=c(1,4)
if(j==3) nums=c(1,5)
if(j==4) nums=c(1,2)
if(j==5) nums=c(1,2,4,6)
if(j==6) nums=c(1,2,5,8)
if(j==7) nums=c(1,3)
if(j==8) nums=c(1,3,4,7)
if(j==9) nums=c(1,3,5,9)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
#ans1
#wt=matrix(1/ans1,byrow=T,nrow=3) # inverse of variance
#wt
# [,1] [,2] [,3]
#[1,] 139.91126 228.6460 29.81521
#[2,] 142.15404 321.5600 38.28501
#[3,] 26.62504 42.6484 6.09793
tb.b=matrix(ans2,byrow=T,nrow=3)
tb.b
row.names(tb.b)=paste(0:2)
colnames(tb.b)=paste(0:2)
tb.b
}# end of if (length(grep("3by3",diseaseModel))!=0)
if(method=="2x3" | length(grep("2by3",method))!=0){
#> betas b0 b1 b2 b3 b4 b5
# Intercept x1 x2_1 x2_2 x1:x2_1 x1:x2_2
#-1.76419540 0.05184397 0.88573685 1.02992382 0.12562113 0.18818496
# table is:
# b0 b0+b2 b0+b3 1 1+3 1+4
# b0+b1 b0+b1+b2+b4 b0+b1+b3+b5 1+2 1+2+3+5 1+2+4+6
#
ans2=rep(NA,length(coeff)) # total 3 by 3 = 9 cells
#tb.b=matrix(ans2,byrow=T,nrow=3)
for(j in 1:length(ans2)){ ## byRow=F
if(j==1) nums=1
if(j==2) nums=c(1,3)
if(j==3) nums=c(1,4)
if(j==4) nums=c(1,2)
if(j==5) nums=c(1,2,3,5)
if(j==6) nums=c(1,2,4,6)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
tb.b=matrix(ans2,byrow=T,nrow=2)
tb.b
row.names(tb.b)=paste(0:1)
colnames(tb.b)=paste(0:2)
tb.b
}#end of
if(method=="3x2" | length(grep("3by2",method))!=0){
#> betas
# xx11 xx12 xx21 xx11:xx21 xx12:xx21
#-0.03771927 -0.02072611 1.11752878 -0.20145361 -0.23867683
# b0 b0+b3 1 1+4
# b0+b1 b0+b1+b3+b4 1+2 1+2+4+5
# b0+b2 b0+b2+b3+b5 1+3 1+3+4+6
ans2=rep(NA,length(coeff)) # total 3 by 3 = 9 cells
#tb.b=matrix(ans2,byrow=T,nrow=3)
for(j in 1:length(ans2)){ ## byRow=T
if(j==1) nums=1
if(j==2) nums=c(1,4)
if(j==3) nums=c(1,2)
if(j==4) nums=c(1,2,4,5)
if(j==5) nums=c(1,3)
if(j==6) nums=c(1,3,4,6)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
tb.b=matrix(ans2,byrow=T,nrow=3)
tb.b
row.names(tb.b)=paste(0:2)
colnames(tb.b)=paste(0:1)
tb.b
#> betas b0 b1 b2 b3 b4 b5
# Intercept x1 x2_1 x2_2 x1:x2_1 x1:x2_2
#-1.76419540 0.05184397 0.88573685 1.02992382 0.12562113 0.18818496
# table is:
# b0 b0+b2 b0+b3 1 1+3 1+4
# b0+b1 b0+b1+b2+b4 b0+b1+b3+b5 1+2 1+2+3+5 1+2+4+6
#
}#end of
tb.b
}# end of function
Try the CGEN package in your browser
Any scripts or data that you put into this service are public.
CGEN documentation built on April 28, 2020, 8:08 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions makeBetaTable.general
makeBetaTable.general=function(betas,method){ ## this construct beta table out of beta coefficient
coeff=betas # betas should include b0
if (method=="2x2" | length(grep("2by2",method))!=0) {
#> vc
# (Intercept) xx11 xx21 xx11:xx21
#(Intercept) 0.007147387 -0.007147387 -0.007147387 0.007147387
#xx11 -0.007147387 0.012507390 0.007147387 -0.012507390
#xx21 -0.007147387 0.007147387 0.010774803 -0.010774803
#xx11:xx21 0.007147387 -0.012507390 -0.010774803 0.018271530
#vars=diag(vc)
#> vars
#(Intercept) xx11 xx21 xx11:xx21
#0.007147387 0.012507390 0.010774803 0.018271530
# b0 b1 b2 b3
# 1 2 3 4
# table is:
# b0 b0+b2 1 1+3
# b0+b1 b0+b1+b2+b3 1+2 1+2+3+4
#
#ans1=rep(NA,4) # total 2 by 2 = 4 cells
ans2=rep(NA,4)
for(j in 1:length(ans2)){
if(j==1) nums=1
if(j==2) nums=c(1,3)
if(j==3) nums=c(1,2)
if(j==4) nums=c(1,2,3,4)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
tb.b=matrix(ans2,byrow=T,nrow=2) # inverse of variance
tb.b
# [,1] [,2] [,3]
#[1,] 139.91126 228.6460 29.81521
#[2,] 142.15404 321.5600 38.28501
#[3,] 26.62504 42.6484 6.09793
}#end of
if (method=="3x3" | length(grep("3by3",method))!=0) { # if 3 by 3 table model
#vars
#(Intercept) xx11 xx12 xx21 xx22 xx11:xx21 xx12:xx21 xx11:xx22 xx12:xx22
#0.007147387 0.014182010 0.030524010 0.011520961 0.029166356 0.021665423 0.050861708 0.052176401 0.117532487
# b0 bg1 bg2 bx1 bx2 d11 d21 d12 d22
# 1 2 3 4 5 ( 6 7 8 9 )
# table is: 0 1 2
# 0 b0 b0+bx1 b0+bx2
# 1 b0+bg1 b0+bg1+bx1+d11 b0+bg1+bx2+d12
# 2 b0+bg2 b0+bg2+bx1+d21 b0+bg2+dx2+d22
# ------> 1 1+4 1+5
# 1+2 1+2+4+6 1+2+5+8
# 1+3 1+3+4+7 1+3+5+9
#coeff
#(Intercept) xx11 xx12 xx21 xx22 xx11:xx21 xx12:xx21 xx11:xx22 xx12:xx22
# -1.2012218 0.2669125 0.7492366 1.0790657 0.6657035 0.7198954 0.1653648 0.6580705 1.5593489
# 1 2 3 4 5 (6 7 8 9)
#ans1=rep(NA,9) # total 3 by 3 = 9 cells
ans2=rep(NA,9) # total 3 by 3 = 9 cells
for(j in 1:length(ans2)){
if(j==1) nums=1
if(j==2) nums=c(1,4)
if(j==3) nums=c(1,5)
if(j==4) nums=c(1,2)
if(j==5) nums=c(1,2,4,6)
if(j==6) nums=c(1,2,5,8)
if(j==7) nums=c(1,3)
if(j==8) nums=c(1,3,4,7)
if(j==9) nums=c(1,3,5,9)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
#ans1
#wt=matrix(1/ans1,byrow=T,nrow=3) # inverse of variance
#wt
# [,1] [,2] [,3]
#[1,] 139.91126 228.6460 29.81521
#[2,] 142.15404 321.5600 38.28501
#[3,] 26.62504 42.6484 6.09793
tb.b=matrix(ans2,byrow=T,nrow=3)
tb.b
row.names(tb.b)=paste(0:2)
colnames(tb.b)=paste(0:2)
tb.b
}# end of if (length(grep("3by3",diseaseModel))!=0)
if(method=="2x3" | length(grep("2by3",method))!=0){
#> betas b0 b1 b2 b3 b4 b5
# Intercept x1 x2_1 x2_2 x1:x2_1 x1:x2_2
#-1.76419540 0.05184397 0.88573685 1.02992382 0.12562113 0.18818496
# table is:
# b0 b0+b2 b0+b3 1 1+3 1+4
# b0+b1 b0+b1+b2+b4 b0+b1+b3+b5 1+2 1+2+3+5 1+2+4+6
#
ans2=rep(NA,length(coeff)) # total 3 by 3 = 9 cells
#tb.b=matrix(ans2,byrow=T,nrow=3)
for(j in 1:length(ans2)){ ## byRow=F
if(j==1) nums=1
if(j==2) nums=c(1,3)
if(j==3) nums=c(1,4)
if(j==4) nums=c(1,2)
if(j==5) nums=c(1,2,3,5)
if(j==6) nums=c(1,2,4,6)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
tb.b=matrix(ans2,byrow=T,nrow=2)
tb.b
row.names(tb.b)=paste(0:1)
colnames(tb.b)=paste(0:2)
tb.b
}#end of
if(method=="3x2" | length(grep("3by2",method))!=0){
#> betas
# xx11 xx12 xx21 xx11:xx21 xx12:xx21
#-0.03771927 -0.02072611 1.11752878 -0.20145361 -0.23867683
# b0 b0+b3 1 1+4
# b0+b1 b0+b1+b3+b4 1+2 1+2+4+5
# b0+b2 b0+b2+b3+b5 1+3 1+3+4+6
ans2=rep(NA,length(coeff)) # total 3 by 3 = 9 cells
#tb.b=matrix(ans2,byrow=T,nrow=3)
for(j in 1:length(ans2)){ ## byRow=T
if(j==1) nums=1
if(j==2) nums=c(1,4)
if(j==3) nums=c(1,2)
if(j==4) nums=c(1,2,4,5)
if(j==5) nums=c(1,3)
if(j==6) nums=c(1,3,4,6)
#ans1[j]= extractVar(vars,nums,vc)
ans2[j]= sum(coeff[nums])
}# end of j loop
tb.b=matrix(ans2,byrow=T,nrow=3)
tb.b
row.names(tb.b)=paste(0:2)
colnames(tb.b)=paste(0:1)
tb.b
#> betas b0 b1 b2 b3 b4 b5
# Intercept x1 x2_1 x2_2 x1:x2_1 x1:x2_2
#-1.76419540 0.05184397 0.88573685 1.02992382 0.12562113 0.18818496
# table is:
# b0 b0+b2 b0+b3 1 1+3 1+4
# b0+b1 b0+b1+b2+b4 b0+b1+b3+b5 1+2 1+2+3+5 1+2+4+6
#
}#end of
tb.b
}# end of function
Try the CGEN package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.